Method and system for microbiome analysis

ABSTRACT

A method and system for analyzing a microbiome of an individual, comprising: providing a sampling kit to the individual at a location remote from the sample processing network, the sampling kit including a sample container having a lysing component and a sample preservation component and configured to receive a sample from a collection site of the individual; receiving the sample container with the sample from the collection site of the individual; generating a microbiome sequence dataset based upon sequencing nucleic acid content of a microorganism portion of the sample; identifying a set of microorganisms represented in the microorganism portion based upon performance of a mapping operation on portions of the microbiome sequence dataset; generating an analysis based upon a set of features related to the microorganism portion; and transmitting information derived from the analysis to the individual.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application Ser.No. 62/024,947 filed 15 Jul. 2014, U.S. Provisional Application Ser. No.61/953,683 filed 14 Mar. 2014, and U.S. Provisional Application Ser. No.61/931,612 filed 25 Jan. 2014, which are each incorporated in itsentirety herein by this reference.

TECHNICAL FIELD

This invention relates generally to the field of microbiology and morespecifically to a new and useful method and system for performingmicrobiome analysis in the field of microbiology.

BACKGROUND

A microbiome is an ecological community of commensal, symbiotic, andpathogenic microorganisms (e.g., bacteria, fungi, archaea, viruses) thatare associated with an organism. The human microbiome comprises over 10times more microbial cells than human cells, but characterization of thehuman microbiome is still in nascent stages due to limitations in sampleprocessing techniques, genetic analysis techniques, and resources forprocessing large amounts of data. Nonetheless, the microbiome issuspected to play at least a partial role in a number ofhealth/disease-related states (e.g., preparation for childbirth,diabetes, auto-immune disorders, gastrointestinal disorders, rheumatoiddisorders, neurological disorders, etc.). Given the profoundimplications of the microbiome in affecting an individual's health,efforts related to the characterization of the microbiome and generationof insights from the characterization should be pursued. Current methodsand systems that attempt to analyze the microbiomes of humans, atindividual and population-wide levels have, however, been largelyunsuccessful, leaving many questions unanswered.

As such, there is a need in the field of microbiology for a new anduseful method and system for performing microbiome analysis. Thisinvention creates such a new and useful method and system.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A is a flowchart of an embodiment of a method for performingmicrobiome analysis;

FIG. 1B is a flowchart of an embodiment of a method for performingmicrobiome analysis for a population of individuals;

FIG. 2 is a schematic of an embodiment of a system for performingmicrobiome analysis;

FIG. 3 is a flowchart of a variation of a portion of a method forperforming microbiome analysis;

FIG. 4A is a schematic of a variation of a sampling kit in a method andsystem for performing microbiome analysis;

FIG. 4B is a schematic of a specific example of a sampling kit in amethod and system for performing microbiome analysis;

FIG. 5A is a flowchart of a variation of a portion of a method forperforming microbiome analysis;

FIG. 5B depicts TABLES 1-4 depicting specific examples of primers andbarcode sequences used in an embodiment of a method for performingmicrobiome analysis;

FIG. 6 is a schematic of a variation of a portion of a system forperforming microbiome analysis;

FIG. 7A is a flowchart of a variation of a portion of a method forperforming multiplex analysis in a method for performing microbiomeanalysis;

FIG. 7B is a schematic of elements used in a method for performingmultiplex analysis;

FIG. 8 is a flowchart of a variation of a portion of a method forperforming microbiome analysis;

FIG. 9A is a flowchart of a variation of a portion of a method forperforming microbiome analysis;

FIG. 9B is a schematic of a variation of a portion of a system forperforming microbiome analysis;

FIG. 10 is a flowchart of a variation of a portion of a method foruniquely identifying samples in a method for performing microbiomeanalysis;

FIGS. 11A and 11B depict aspects of a variation of a portion of a methodfor uniquely identifying samples and quantifying nucleic acid content ina method for performing microbiome analysis;

FIG. 12 is a flowchart of a variation of a portion of a method forperforming microbiome analysis;

FIG. 13 is an example of a survey, provided by way of a socialnetworking system, in a variation of a method for performing microbiomeanalysis;

FIG. 14 is a schematic of a portion of a method for performingmicrobiome analysis;

FIGS. 15A-15F depict examples of visualization tools and user interfacesfor providing microbiome-derived insights to individuals in anembodiment of a method and system for performing microbiome analysis;and

FIG. 16 depicts an example of a hashing operation in an embodiment of amethod and system for performing microbiome analysis.

DESCRIPTION OF THE EMBODIMENTS

The following description of the embodiments of the invention is notintended to limit the invention to these embodiments, but rather toenable any person skilled in the art to make and use this invention.

1. Method and System

As shown in FIG. 1A, a method 100 for analyzing a microbiome of anindividual comprises: providing a sampling kit to the individual, thesampling kit including a sample container having a process reagentcomponent and configured to receive a sample from a collection site ofthe individual S100; at a sample handling network, receiving the samplecontainer with the sample from the collection site of the individualS120; at a sample processing module within the sample handling network,generating a microbiome sequence dataset based upon sequencing nucleicacid content of a microbiome portion of the sample S130; at a processingsystem within the sample handling network, identifying a set ofmicroorganisms represented in the microbiome portion based uponperformance of a mapping operation on portions of the microbiomesequence dataset S140; at the processing system, generating an analysisbased upon a set of features related to the microorganism portion S150;and from the processing system, transmitting information derived fromthe analysis to the individual S160.

The method 100 is preferably configured to be expanded to a populationof individuals, as shown in FIG. 1B, such that an expanded method 100′can include: providing sampling kits to a population of individuals,each sampling kit including a sample container having a lysing componentand a sample preservation component and configured to receive a samplefrom a collection site of an individual of the set of individuals S100′;at a sample handling network, receiving sample containers with samplesfrom the population of individuals S120′; at a sample processing modulewithin the sample handling network, generating a microbiome sequencedataset for each individual in the population of individuals, whereinthe microbiome sequence dataset for an individual is generated basedupon sequencing nucleic acid content of a microorganism portion of asample from the individual S130′; at a processing system within thesample handling network, identifying a set of microorganisms representedin the microorganism portion of each microbiome sequence dataset, basedupon performance of a mapping operation on each microbiome sequencedataset S140′; at the processing system, generating an analysis basedupon a set of features related to the microorganism portion for eachmicrobiome sequence dataset S150′; and from the processing system,transmitting information derived from the analysis to each of thepopulation of individuals S160′.

The method 100 functions to generate and provide insights derived fromcompositional aspects of the microbiomes of one or more individuals, andto provide means for efficient sample reception and processing from theindividual(s). In variations, blocks of the method 100 can be configuredto guide the sample provision and/or reception process for individualswho are at locations remote from a sample handling network, can beconfigured to enable unique identification of individual samplescollected from a population of individuals, mitigate or prevent samplecontamination (e.g., cross contamination, etc.), and/or can beconfigured to more efficiently process samples in a multiplex manner.Insights derived from outputs of the method 100 can also be used toclassify individuals based upon microbiome-based analyses conducted atan individual and/or a population level.

In one application, the method 100 is implemented at least in part at asystem 200, as shown in FIG. 2, including a sample handling network 210that facilitates provision of sampling kits 220 to individuals using adistribution service 215, receives biological samples from theindividuals by way of the sample reception kit, processes the biologicalsamples at a sample processing module 230 within the sample handlingnetwork, performs microbiome-based analyses on sequenced nucleic acidcontent of the biological samples at a processing system 240 within thesample handling network, and transmits information derived from themicrobiome-based analyses to individuals in cooperation with a socialnetworking system 250. The method 100 can, however, alternatively beimplemented using any other suitable system(s) configured to receive andprocess microbiome-related data of users, in aggregation with otherinformation, in order to generate and share insights derived frommicrobiome-based analyses conducted at individual and/or population-widelevels.

1.1 Sample Provision

Block S100 recites: providing a sampling kit to the individual, thesampling kit including a sample container having a process reagentcomponent and configured to receive a sample from a collection site ofthe individual. Block S110 functions to provide a mechanism by which anindividual, who is at a location remote from a sample handling network,can provide samples in a dependable manner. In Block S110, providing thesampling kit is preferably performed using a parcel delivery service(e.g., postal service, shipping service, mailing service, etc.)accessible to the sample handling network, such that the sample handlingnetwork can provide the sampling kit(s) to one or more individuals overthe parcel delivery service. Additionally or alternatively, the samplingkit can additionally or alternatively be provided directly through anentity associated with the sample handling network, wherein the entityis also trained to facilitate sample reception from an individual. Inexamples, the entity can be any one or more of: a clinical technician, alaboratory technician, a healthcare professional (e.g., doctor, nurse,etc.), and any other suitable entity that can facilitate provision ofthe sampling kit to an individual or facilitate reception of a samplefrom the individual by way of the sampling kit. However, provision ofthe sampling kit(s) to the individual(s) in Block S110 can additionallyor alternatively be performed in any other suitable manner.

The sampling kit(s) provided in Block S100 are preferably configured tofacilitate reception of samples from individuals in a non-invasivemanner. In variations, non-invasive manners of sample reception from anindividual can use any one or more of: a permeable substrate (e.g., aswab configured to wipe a region of an individual's body, toilet paper,a sponge, etc.), a non-permeable substrate (e.g., a slide, tape, etc.) acontainer (e.g., vial, tube, bag, etc.) configured to receive a samplefrom a region of an individual's body, and any other suitablesample-reception element. In a specific example, samples can becollected from one or more of an individual's nose, skin, genitals,mouth, and gut in a non-invasive manner (e.g., using a swab and a vial).However, the sampling kit(s) provided in Block S110 can additionally oralternatively be configured to facilitate reception of samples in asemi-invasive manner or an invasive manner. In variations, invasivemanners of sample reception can use any one or more of: a needle, asyringe, a biopsy element, a lance, and any other suitable instrumentfor collection of a sample in a semi-invasive or invasive manner. Inspecific examples, samples from individuals can comprise one or more of:blood samples, plasma/serum samples (e.g., to enable extraction ofcell-free DNA), and tissue samples.

In Block S110, providing the sampling kit to an individual can furtherinclude one or more of: providing instructions to an individualregarding provision of the sample S111, providing instructions to anindividual regarding pre-processing of the sample S112, and providinginstructions to an individual regarding setting up a user account withina social networking system configured to provide microbiome-derivedinsights to the individual S113, as shown in FIG. 3. Blocks S111, S112,and S113 function to guide a remote individual in providing one or moresamples in a dependable manner, guide a remote individual in performingsome aspects of sample pre-processing (e.g., with the individual'sacknowledgement, in a surreptitious manner without the individual'sacknowledgement), and guide a remote individual in setting up apersonalized account at which the individual can receive informationrelated to his/her microbiome, respectively.

In variations of Block S111, providing instructions regarding provisionof the sample can include one or more of: providing sample provisioninstructions specific to one or more of a set of collection sites of thebody of an individual, providing instructions pertaining to an amount ofsample to be provided by the individual, providing instructionspertaining to time(s) of day at which to provide samples, providinginstructions pertaining to behaviors that should be avoided prior toand/or during sample provision, providing instructions pertaining tobehavior that are encouraged prior to and/or during sample provision,providing instructions regarding correction of an improperly providedsample, providing instructions regarding storage of a sample prior totransmission to a sample handling network (e.g., with regard totemperature ranges at which to store a sample, with regard toorientation of a sample container, with regard to motion of a samplecontainer, etc.), instructions regarding transmission of a sample to asample handling network, and provision of any other suitableinstructions related to sample provision.

In a specific example of Block S111, instructions for sample provisioncan be provided for collection sites associated with the gut, the skin,the mouth, the nose, the male genitals, and the female genitals. Withregard to the gut, instructions for sample provision in the specificexample include swabbing used toilet paper to collect a small amount offeces (e.g., enough to change the color of the swab). With regard to theskin, instructions for sample provision in the specific example includewetting a swab provided in the sampling kit with polymerase chainreaction (PCR) water provided in the sampling kit, and wiping the wettedswab along the lower half of the crease behind the ear for one minute(e.g., while pulling the ear forward or pulling hair out of the way, ifnecessary). With regard to the mouth, instructions for sample provisionin the specific example include swabbing the inside of each cheekvigorously for 30 seconds, without touching the swab to the teeth orgums. With regard to the nose, instructions for sample provision in thespecific example include wetting a swab provided in the sampling kitwith polymerase chain reaction (PCR) water provided in the sampling kit,and wiping the wetted swab within each nostril at the depth of the swabfor 30 seconds. With regard to the male genitals, instructions forsample provision in the specific example include wetting a swab providedin the sampling kit with polymerase chain reaction (PCR) water providedin the sampling kit, and wiping the wetted swab in a circular motionaround the base of the head of the penis for one minute (e.g., withpulling back of the foreskin, if necessary). With regard to the femalegenitals, instructions for sample provision in the specific exampleinclude wetting a swab provided in the sampling kit with polymerasechain reaction (PCR) water provided in the sampling kit, and wiping thewetted swab in the area just inside the vaginal opening, to the depth ofcotton on the swab, for one minute (e.g., with spreading of the labiausing the hand not performing the swabbing motion).

In the specific example of Block S111, provided instructions includeinstructions to avoid sample contamination (e.g., by advising anindividual to place caps of sample containers upside down in order toavoid transmitting a contaminant into the interior of the samplecontainer). In the specific example, provided instructions furtherinclude instructions to avoid bathing or bringing substances that mightdisturb the microbiome into contact with a sample site for at least 8hours prior to sample provision by an individual. In the specificexample, the instructions further advise against contact withantiseptics antibiotic soaps, and lotions, and behaviors such as teethbrushing, using mouthwash, kissing, sex, hot tubbing, eating, swimming,and any behaviors that could disturb the microbiome of the individual.In the specific example, instructions include instructions regardingpackaging of sample containers including collected samples prior totransmission to a sample handling network (e.g., using a parcel deliveryservice), and first aid instructions in the event of inappropriateusage. Variations of the specific example of Block S111 can, however,include any other suitable instructions related to sample provision.

In variations of Block S112, providing instructions regardingpre-processing of the sample can include one or more of: instructionspertaining to lysis of cells of a provided sample, instructionspertaining to incubation of cells of a provided sample, instructionspertaining to mixing a provided sample with process reagents prior totransmission to a sample handling network, and any other suitableinstructions related to pre-processing of a biological sample. In aspecific example of Block S112, the individual providing the sample isinstructed to combine a sample on a swab with process reagentspre-packaged in a sample container provided by the sampling kit, bystirring the swab within the sample container for a minute withoutsplashing contents of the sample container. In the specific example ofBlock S112, the individual is further instructed to shake the samplecontainer with the process reagents and the sample for one minute, inorder to begin a process of cell lysing within the sample and nucleicacid extraction from the sample. In Block S112, instructing theindividual in pre-processing the sample can be conducted in an openmanner wherein the individual is aware that he/she is involved in thesample pre-processing process, or alternatively in a surreptitiousmanner with the individual unaware that he/she is involved in the samplepre-processing process.

In variations of Block S113, providing instructions regarding setting upa user account within a social networking system configured to providemicrobiome-derived insights to the individual can include providing auniform resource locator (URL) or other internet address by which anindividual can set up an account within an online social networkingsystem. Provision of an address can be performed using a messagingclient (e.g., a text messaging client, an email messaging client, etc.),using textual-based instructions provided within the sampling kit, usinga machine-decodable tag (e.g., a QR code, a barcode, an antennaassociated with a near field communication device, etc.), and/or in anyother suitable manner. Instructions provided in association with BlockS113 can further include instructions regarding initialization of anaccount (e.g., by providing a user name and a password), instructionsregarding provision of personal information, instructions regardingassociating a user account with an identifying aspect (e.g.,registration ID) of a sampling kit, and any other suitable instructions.Information needed from the individual in setting up the user accountcan, in Block S113, be directly input by individual (e.g., using aninput device of an electronic device associated with the individual),and can additionally or alternatively be automatically populated basedupon accessing information databases associated with the individual. Forinstance information needed in setting up the user account can bepopulated upon accessing of an electronic health record (EHR) and/or asocial network accounts (e.g., Facebook account, LinkedIn account,Twitter account, etc.) associated with the individual, upon receivingpermission from the individual.

In any one or more of Blocks S111, S112, and S113, instruction provisioncan include one or more of: text-based instruction provision,picture-based instruction, video-based instruction provision,audio-based instruction provision, touch/haptic-based instructionprovision, and any other suitable form of instruction provision. Forinstance, Blocks S111, S112, and/or S113 can include providing text andpicture-based instructions on a card included with the sampling kit, orinstructions included with an electronic storage device (e.g., memorycard, disk, etc.). Additionally or alternatively, Block S113 canfacilitate the instruction provision process, whereby text, picture,audio, and/or video-based instructions can be provided through the useraccount of the social networking system. For instance, once anindividual has logged into his/her user account at an electronic deviceincluding input devices (e.g., a keyboard, a touch screen, a mouse, atouch pad, a microphone, a camera, etc.) and output devices (e.g., adisplay, a speaker, a vibration module, etc.), the electronic device canfacilitate instruction provision as the individual interfaces with thesocial networking system.

As noted above, Block S100 is preferably implemented by way of a system200, as shown in FIG. 2, that includes a sample handling network 210that facilitates provision of sampling kits 220 to individuals. Thesample handling network 210 thus functions as a platform from whichsampling kits can be distributed to individuals who are remote from thesample handling network, and to which sample containers includingsamples from individuals can be returned for processing and analysis.One aspect of the sample handling network 210 thus functions as adistribution and receiving hub for biological sample handling, whereinindividuals are able to transmit samples directly to the sample handlingnetwork without requiring direct contact between individuals and aclinical or laboratory-based intermediary staffed with trained personnelfor biological sample handling. The sample handling network 210 is thuspreferably configured to provide instructions directly to individualspertaining to sample provision in a dependable manner without involvinglaboratory-trained personnel in the sample provision process, and ispreferably configured to associate samples with individuals providingthe samples in a secure and reliable manner that is compliant withregulatory standards (e.g., compliant with the Health InsurancePortability and Accountability Act, HIPAA). However, the sample handlingnetwork 210 can alternatively be configured to distribute sampling kits220 and/or receive samples from individuals using a laboratory-based orclinical-based intermediary, and/or handle samples in any other suitablemanner.

The sampling kit(s) 220 provided by way of the sample handling network210 preferably include at least sample extraction element (e.g.,permeable substrate, non-permeable substrate, swab, toilet paper,sponge, lancet, needle, syringe, etc.), at least one sample container(e.g., sample chamber, vial, well, etc.), instructions (e.g., asdescribed in relation to Blocks S111, S112, and S113 above), sampleprovision reagents, sample process reagents, and features configured tofacilitate association of the sampling kit and sample container(s) ofthe sampling kit with an individual providing the sample(s). Invariations, the process reagent components can include a lysingcomponent (e.g., beads, lysing reagents, etc.) and a sample preservationcomponent; however, in other variations, the process reagent can includeany other suitable process reagent that facilitates sample handling. Thesampling kit(s) also preferably include packing elements that enable theindividual to transmit a provided sample to the sample handling network210. The sampling kit(s) 220 can additionally or alternatively includeelements that prevent sample contamination (e.g., sample isolationelements), elements that promote hygiene of the individualpost-provision of a sample (e.g., alcohol wipes, antibacterial wipes,lotions, soaps, etc.), and/or any other suitable elements thatfacilitate an individual prior to, during, and/or post provision of asample.

As such, in one variation, as shown in FIG. 4A, the sampling kit 220 caninclude a permeable substrate 221 (e.g., a swab) configured tofacilitate extraction of a sample from a dedicated collection site ofthe individual's body (or an object that contacts the individual), and asample process reagent (e.g., PCR water) configured to permeate thepermeable substrate 221 in variations wherein a wetted permeablesubstrate would facilitate sample extraction from an individual. In thevariation, the permeable substrate(s) 221 and the sample process reagentare preferably packaged in a sterile manner, in order to avoid samplecontamination. In a specific example, the sampling kit 220 includes aset of swabs as permeable substrates 221, wherein each swab is sealed ina container in a sterile manner. In the specific example, the samplingkit 220 further includes a set of vials 222 of a PCR water for wettingone or more swabs of the set of swabs, wherein each vial is also sealed,prior to use by the individual, in a sterile manner.

Variations of the sample container(s) 223 provided with the sampling kit220 can include sample chambers, vials, well-plates, and/or any othersuitable sample containing element. A sample container 223 provided withthe sampling kit 220 is preferably configured to have a sufficientvolume for reception of a sample (e.g., by way of a permeablesubstrate), and/or mixing of the sample with sample processing reagentswithin the sample container 223. Additionally, a sample container 223provided with the sampling kit 220 can be pre-packaged with sampleprocessing reagents (e.g., sample lysis beads, sample lysis reagents,nucleic acid amplification reagents), and/or sample preservationreagents (e.g., reagents for preservation of nucleic acids).Additionally or alternatively, sample containers and/or any othersuitable element of the sampling kit 220 can facilitate sample handlingprocesses associated with one or more of: sample freezing (e.g.,cryogenic freezing), sample lyophilization, active culture of a sample,and any other suitable downstream sample handling process. Furthermore,sample containers 223 provided in the sampling kit 220 can includeunique identifying features (e.g., colors, textures, shapes, labels,etc.) associated with collection sites of the individual, that enablethe individual to provide a sample within the correct sample container223 with a reduced chance of error. In a specific example, as shown inFIG. 4B, the sampling kit 220′ includes a set of color-coded vials(i.e., color coded and labeled according to collection site) as samplecontainers 223′ for sample reception, wherein each vial includesTris(hydroxymethyl)aminomethane (e.g., at a concentration of ≤1.8%) forbuffering a sample, sodium chloride (e.g., at a concentration of ≤8%),Edetate disodium dehydrate (e.g., at a concentration of ≤18.6%) as achelating agent, and guanidine thiocyanate (e.g., at a concentration of≤2M) as a chaotropic agent for solubilizing cells. Variations of thespecific example can additionally or alternatively include additionalreagents for sample preservation, reagents that prepare the sample forfurther processing (e.g., reagents for amplification), and/or any othersuitable reagents.

In variations wherein portions of the sampling kit 220 for samplereception (e.g., sample containers 223) are configured to be deliveredback to the sample handling network 210, the sampling kit 220 canfurther include a packaging receptacle 224 (e.g., a bubble mailer, anenvelope, a parcel, etc.), with or without postage for delivery to thesample handling network 110. Additionally or alternatively, portions ofthe sampling kit can be configured to be picked up by a courier servicespecifically associated with the sample handling network (e.g., using astaff of couriers configured to be contacted when a sample from anindividual is ready to be picked up), wherein the individual is giveninstructions to contact the courier service once provision of a sampleis complete. The sample delivery process can, however, be facilitated bythe sampling kit 220 in any other suitable manner.

Identifying features 225 of the sampling kit 220 can include one or moreof: a registration code of characters (e.g., alphanumeric characters), abiological identifier (e.g., a nucleic acid marker with a specificsequence and/or a specific concentration), a machine-readable tag (e.g.,QR code, barcode, antenna detectable using a near field communicationdevice, etc.), and any other suitable identifier. Furthermore, thesampling kit 220 can include or be configured to facilitate instructionprovision to an individual, as described in relation to Blocks S111,S112, and S113 above. Variations of elements of the sampling kit 220configured for instruction provision can include printed materialsand/or digitally stored information (e.g., information stored inmemory), and/or can comprise a link, code, or reference todigitally-stored information (e.g., a link to a program, a file, or anapplication). In some variations, the sampling kit can be configured tofacilitate instruction provision by way of an electronic deviceassociated with the individual. For instance, a QR code of the samplingkit 220 can be scanned using an electronic device of the individual,wherein the QR code links to an address that includes text and visualinstructions for sample provision. In another example, a printed card inthe sampling kit 220 can include a URL at which instructions for sampleprovision are provided to the individual. Identifying features andelements of the sampling kit 220 associated with instruction provisioncan, however, be configured in any other suitable manner.

Variations of the sampling kit(s) 220 and/or the sample handling network210 can, however, comprise any other suitable elements and/or beconfigured in any other suitable manner.

1.2 Sample Reception

Block S120 recites: at a sample handling network, receiving the samplecontainer with the sample from the collection site of the individual,which functions to enable generation of data from which microbiome-basedinsights for an individual and/or for a population of individuals can bederived. As noted above, reception of sample containers in Block S120can be facilitated using one or more of a parcel delivery service and acourier service, or can alternatively be directly enabled with deliveryof a sample container to the sample handling network by the individualassociated with the sample container. Furthermore, samples received inBlock S120 can be in a pre-processed state of lysing (i.e., due toagitation of a sample by an individual in Block S110), or canalternatively be in any other suitable state upon reception at thesample handling network.

In Block S120, an aggregate set of samples is preferably received from awide variety of individuals, using an aggregate set of sampling kitsprovided to the individuals by way of the sample handling network.Preferably, the wide variety of individuals includes individuals of oneor more of: different demographics (e.g., genders, ages, maritalstatuses, ethnicities, nationalities, socioeconomic statuses, sexualorientations, etc.), different health conditions (e.g., health anddisease states), different living situations (e.g., living alone, livingwith pets, living with a significant other, living with children, etc.),different dietary habits (e.g., omnivorous, vegetarian, vegan, sugarconsumption, acid consumption, etc.), different behavioral tendencies(e.g., levels of physical activity, drug use, alcohol use, etc.),different levels of mobility (e.g., related to distance traveled withina given time period), and any other suitable trait that has an effect onmicrobiome composition. As such, as the number of individuals increases,the power of insights generated in subsequent blocks of the method 100increases, in relation to characterizing of a variety of individualsbased upon their microbiomes. Additionally or alternatively, the samplesreceived in Block S120 can include receiving biological samples from atargeted group of similar individuals in one or more of: demographictraits, health conditions, living situations, dietary habits, behaviortendencies, levels of mobility, and any other suitable trait that has aneffect on microbiome composition, such that insights generated insubsequent blocks of the method 100 are insights targeted to specificgroups of individuals. Preferably, the set of individuals from whichsamples are received includes individuals who do not have specificresearch training, clinical training, and/or laboratory training, suchthat the samples also represent non-trained individuals, who have beeninstructed in methods of providing samples in a dependable manneraccording to embodiments, variations, and examples of Block S100.However, Block S120 can alternatively include receiving samples from anysuitable group of individuals, using any other suitable sample handlingnetwork-sample delivery service relationship.

In one such alternative variation, reception of sample containers withsamples in Block S120 can be facilitated using a laboratory-based or aclinical-based intermediary that has staff trained in sample extractionfrom an individual and transmission of extracted samples to the samplehandling network. However, reception of the sample at the samplehandling network can be enabled in Block S120 in any other suitablemanner.

1.3 Sample Processing—Amplification and Sequencing

Block S130 recites: at a sample processing module within the samplehandling network, generating a microbiome sequence dataset based uponsequencing nucleic acid content of a microorganism portion of thesample. Block S130 functions to process each sample received in BlockS120, in order to determine microbiome compositional aspects at thelevel of an individual and/or the level of a population of individuals.Compositional aspects can include compositional aspects at themicroorganism level, including parameters related to distribution ofmicroorganisms across different taxonomic groups of phyla, classes,orders, families, genera, and/or species (e.g., as measured in totalabundance of each group, relative abundance of each group, total numberof groups represented, etc.). Compositional aspects can additionally oralternatively include compositional aspects at the genetic level (e.g.,in relation to 16S sequences, in relation to 18S sequences, in relationto ITS sequences, in relation to other genetic markers, etc.). Outputsof Block S130 can thus be used to identify features of interest whichcan be used to characterize the microbiomes of individuals andpopulations of individuals, wherein the features can bemicroorganism-based (e.g., presence of a genus of bacteria),genetic-based (e.g., based upon representation of specific geneticregions and/or sequences), and/or based at any other suitable scale.

Characterizing the microbiome composition associated with a samplepreferably includes a combination of sample processing techniques (e.g.,wet laboratory techniques) and computational techniques (e.g., utilizingtools of bioinformatics) to quantitatively and/or qualitativelycharacterize the microbiome associated with a sample from an individual.

In variations, as shown in FIG. 5A, sample processing in Block S130 canthus include any one or more of: lysing a sample S31, disruptingmembranes in cells of a sample S32, separation of undesired elements(e.g., RNA, proteins) from the sample S33, purification of nucleic acids(e.g., DNA) in a sample to generate a nucleic acid sample comprisingnucleic acid content of a microbiome of the individual and nucleic acidcontent of the individual S34, amplification of nucleic acids from thenucleic acid sample S35, further purification of amplified nucleic acidsof the nucleic acid sample S36, and sequencing of amplified nucleicacids of the nucleic acid sample S37.

In variations, lysing a sample S31 and/or disrupting membranes in cellsof a sample S32 preferably includes physical methods (e.g., beadbeating, nitrogen decompression, homogenization, sonication) of celllysing/membrane disruption, which omit certain reagents that producebias in representation of certain microorganism groups upon sequencing.Additionally or alternatively, lysing or disrupting in Blocks S31 or S32can involve chemical methods (e.g., using a detergent, using a solvent,using a surfactant, etc.). Blocks S31 and S32 can thus function tocomplete lysis of components of a sample, in variations wherein thesample has been received at the sample handling network in apre-processed state of lysis. In variations, separation of undesiredelements from the sample S33 can include removal of RNA using RNasesand/or removal of proteins using proteases. In variations, purificationof nucleic acids in a sample to generate a nucleic acid sample S34 caninclude one or more of: precipitation of nucleic acids from thebiological samples (e.g., using alcohol-based precipitation methods),liquid-liquid based purification techniques (e.g., phenol-chloroformextraction), chromatography-based purification techniques (e.g., columnadsorption), purification techniques involving use of bindingmoiety-bound particles (e.g., magnetic beads, buoyant beads, beads withsize distributions, ultrasonically responsive beads, etc.) configured tobind nucleic acids and configured to release nucleic acids in thepresence of an elution environment (e.g., having an elution solution,providing a pH shift, providing a temperature shift, etc.), and anyother suitable purification techniques.

In variations, amplification of nucleic acids from the nucleic acidsample S35 preferably includes one or more of: polymerase chain reaction(PCR)-based techniques (e.g., solid-phase PCR, RT-PCR, qPCR, multiplexPCR, touchdown PCR, nanoPCR, nested PCR, hot start PCR, etc.),helicase-dependent amplification (HDA), loop mediated isothermalamplification (LAMP), self-sustained sequence replication (3SR), nucleicacid sequence based amplification (NASBA), strand displacementamplification (SDA), rolling circle amplification (RCA), ligase chainreaction (LCR), and any other suitable amplification technique. Inamplification of purified nucleic acids, the primers used are preferablyselected to prevent or minimize amplification bias, as well asconfigured to amplify nucleic acid regions/sequences (e.g., of the 16Sregion, the 18S region, the ITS region, etc.) that are informativetaxonomically and phylogenetically. Thus, universal primers (e.g., aF27-R338 primer set, a F515-R806 primer set, etc.) configured to avoidamplification bias can be used in amplification. Primers used invariations of Block S35 can additionally or alternatively includeincorporated barcode sequences specific to each biological sample, asdescribed in further detail below, which can facilitate identificationof biological samples post-amplification. Primers used in variations ofBlock S35 can additionally or alternatively include adaptor regionsconfigured to cooperate with sequencing techniques involvingcomplementary adaptors (e.g., Illumina Sequencing). Primers used invariations of Block S35 can additionally or alternatively be configuredto target stable nucleic acid regions (e.g., conserved regions, regionsnot prone to mutation) flanking unstable one or more regions (e.g.,mutation-prone regions). Primers used in amplification can, however, beconfigured in any other suitable alternative manner.

In one example, forward primers for amplification can be designed asshown in Table 1 of FIG. 5B, reverse primers for amplification can bedesigned as shown in Table 2 of FIG. 5B, and barcode sequences can bedesigned as shown in Tables 3 and 4 of FIG. 5B, where “F idx” refers toa sequence corresponding to a forward index of an Illumina MiSeq/HiSeqplatform; “i5” refers to a forward barcode sequence; transposase refersto a sequence corresponding to a transposase binding site for anIllumina MiSeq/HiSeq platform; “linker” refers to a zero, one, or twobase fragment configured to reduce homogeneity and improve sequencingresults, “N*” refers to a random base configured to reduce homogeneityand improve sequence results; “16Sv4F” refers to a sequence fortargeting a specific target region of nucleic acid material, such as a16Sv4 region, an ITS region, or an 18S region; “R idx” refers to asequence corresponding to a reverse index of an Illumina MiSeq/HiSeqplatform; and “i7” refers to a reverse barcode sequence. In the example,the forward and reverse barcode sequences comprise a dual indexingsystem, which can allow for sequencing 480 unique sequencing librariesusing a combination of 100 primers.

In some variations, Block S35 can include generation of one or moresequencing libraries, which functions to consolidate amplificationproducts for sequencing, for further analysis, reference, and/orprocessing. In generating sequencing libraries, amplification productscan be normalized based upon an amount of nucleic acid in eachamplification product. For example, the amount of each amplificationproduct added to a sequencing library can be inversely proportional tothe amount of nucleic acid in each amplification product, such thatapproximately the same amount of nucleic acid from each amplificationproduct is added to the sequencing library. Sequencing libraries can befurther consolidated into larger sequencing libraries, and similar togeneration of a sequencing library, the amount of each sequencinglibrary added to a larger sequencing library can be normalized. In ananalogous example, the amount of each sequencing library added to thelarger sequencing library can be inversely proportional to the amount ofnucleic acid in each sequencing library, so that approximately the sameamount of nucleic acid from each sequencing library is added to thelarger sequencing library. Sequencing libraries can, however, begenerated and/or consolidated in any other suitable manner in variationsof Block S35.

In variations, sequencing of amplified nucleic acids of the nucleic acidsample S37 can include methods involving targeted amplicon sequencingand/or metagenomic sequencing, implementing techniques including one ormore of: sequencing-by-synthesis techniques (e.g., Illumina sequencing),capillary sequencing techniques (e.g., Sanger sequencing),pyrosequencing techniques, single-molecule real-time (SMRT) techniques,sequencing by ligation (e.g., SOLiD) techniques, reversible terminatorsequencing techniques, proton detection sequencing techniques, ionsemiconductor (e.g., Ion Torrent) sequencing techniques, nanoporesequencing techniques, electronic sequencing techniques, and any othersuitable type of sequencing technique. Sequencing in Block S37 can beconducted in a manner whereby multiple samples are sequenced inparallel, are sequenced multiple times (e.g., to ensure an adequatenumber of reads per sample), and/or are sequenced in any other suitablemanner.

In a specific example, amplification and sequencing of nucleic acidsfrom a sample includes: solid-phase PCR involving bridge amplificationof DNA fragments of the biological samples on a substrate with oligoadapters, wherein amplification involves primers having a forward indexsequence (e.g., corresponding to an Illumina forward index forMiSeq/HiSeq platforms), a forward barcode sequence, a transposasesequence (e.g., corresponding to a transposase binding site forMiSeq/HiSeq platforms), a linker (e.g., a zero, one, or two-basefragment configured to reduce homogeneity and improve sequence results),an additional random base, a sequence for targeting a specific targetregion (e.g., 16S region, 18S region, ITS region), a reverse indexsequence (e.g., corresponding to an Illumina reverse index forMiSeq/HiSeq platforms), and a reverse barcode sequence. In the specificexample, sequencing comprises Illumina sequencing (e.g., with a HiSeqplatform, with a MiSeq platform) using a sequencing-by-synthesistechnique.

Aspects of sample processing in Block S130 can be performed incoordination with microbiome standards that include a known quantityand/or distribution of microorganisms (e.g., in terms of cell count, interms of cell mass, in terms of number of colony forming units). Forexample, microbiome standards used in Block S130 can include adistribution of from 10-1,000,000 colony forming units (CFUs) of aspecies, and from 1-10 different species of microorganisms. In aspecific example, microbiome standards are prepared with 10,000 CFUs ofBacillus subtilis, 100,000 CFUs of Legionella pneumophilia, 200 CFUs ofClostridium perfringens, 100 CFUs of Enterococcus faecalis, and buffer.In the example, the buffer can comprise Tris(hydroxymethyl)aminomethane(e.g., at a concentration of ≤1.8%), sodium chloride (e.g., at aconcentration of ≤8%), Edetate disodium dehydrate (e.g., at aconcentration of ≤18.6%), and guanidine thiocyanate (e.g., at aconcentration of ≤2M), similar to that provided in examples of thesample containers described in relation to Block S100 above; however,the buffer and/or the microbiome standards used in Block S130 canadditionally or alternatively comprise any other suitablemicroorganisms, any other suitable amounts of microorganisms, any othersuitable relative distributions of microorganisms, and/or any othersuitable buffer.

Furthermore, some aspects of sample processing (e.g., lysis, incubation)in Block S130 can be performed substantially simultaneously with sampleprovision in Block S110 and/or sample reception in Block S120; however,aspects of sample processing (e.g., amplification, sequencing, etc.) canalternatively be performed in a manner that is distinct from Blocks S110and/or S120 of the method 100. Furthermore, some variations of sampleprocessing can include further purification of amplified nucleic acids(e.g., PCR products) prior to sequencing, which functions to removeexcess amplification elements (e.g., primers, dNTPs, enzymes, salts,etc.). In examples, additional purification can be facilitated using anyone or more of: purification kits, buffers, alcohols, pH indicators,chaotropic salts, nucleic acid binding filters, centrifugation, and anyother suitable purification technique.

As noted above, Block S130 is preferably implemented by way of a system200, as shown in FIGS. 2 and 6, that includes a sample processing module230 configured to process samples within the sample handling network210. The sample processing module 230 can comprise a laboratoryenvironment 30 (e.g., wet laboratory environment) within sample handlingnetwork 210, wherein samples in sample containers received at the samplehandling network 210 are transmitted within the sample handling network210 to the sample processing module 230 for sample processing (e.g.,purification of nucleic acid content, amplification of nucleic acidcontent, sequencing of nucleic acid content). The sample processingmodule 230 is preferably implemented entirely within the sample handlingnetwork 210, but can additionally or alternatively include sub-modulesthat are implemented within the sample handling network 210 (e.g., in an“in house” manner) and sub-modules that are implemented outside of thesample handling network 210 (e.g., in an “out of house” manner). In onevariation, sample purification can be performed at a first sub-module ofthe sample processing module 230 within the sample handling network 210,amplification can be performed at a second sub-module of the sampleprocessing module 230 outside of the sample handling network 210, andsequencing can be performed at a third sub-module of the sampleprocessing module 230 outside of the sample handling network 210. Thesample processing module 230 and sub-modules thereof can, however, beconfigured in any other suitable manner in relation to the samplehandling network 210.

For sample processing and purification to extract and isolate nucleicacid content of a biological sample, the sample processing module 230preferably comprises an environment 30 (e.g., sterilized laboratoryhood, sterilized room) sterilized of any contaminating substances (e.g.,substances that could affect nucleic acids in a sample or contribute tocontaminant nucleic acids), wherein sample processing is conducted. Theenvironment 30 can be temperature controlled, controlled for oxygencontent, controlled for carbon dioxide content, and/or controlled forlight exposure (e.g., exposure to ultraviolet light). The environment 30can further comprise a lysing module 231 configured to disrupt cellularmembranes and facilitate nucleic acid release from microorganism cellsin a sample. In one variation, the lysing module 231 can include a beadmilling apparatus (e.g., a Tissue Lyser) configured for use with beadsthat are mixed with a sample and function to agitate biological contentof the sample. Alternatively, the lysing module 231 can comprise acombination of one or more of: lysing reagents (e.g., proteinases),heating modules, and any other suitable apparatus(es) for lysing. Forisolation of nucleic acids from a lysed sample, the environment caninclude a purification module 232 for separation of non-nucleic acidcontent of a sample from nucleic acid content of a sample. Apurification module 232 of the sample processing module 230 can operatebased upon force-based separation, sized-based separation,binding-moiety-based separation (e.g., with magnetic binding moieties,with buoyant binding moieties, etc.), and/or any other suitable form ofseparation. For instance, a purification module 232 can include one ormore of: a centrifuge to facilitate extraction of a supernatant, afilter (e.g., a filtration plate), a fluid delivery module configured tocombine a lysed sample with moieties that bind to nucleic acid contentand/or waste material of a sample, a wash reagent delivery system, anelution reagent delivery system, and any other suitable apparatus forpurification of nucleic acid content from a sample.

For nucleic acid amplification, the sample processing module 230preferably comprises amplification substrates 233 (e.g., PCR-compatiblesample-receiving substrates) and a thermocycling module 234 configuredto perform thermocycling on the amplification substrates 233, whereinthe amplification substrates 233 are configured to receive one or moresamples (e.g., lysed samples), primer solutions, reagents (e.g., amaster mix, PCR water), and any other suitable materials for nucleicacid amplification. The thermocycling module 234 can be configured tothermocycle different amplification substrates according toindividualized thermocycling sequences (e.g., temperatures, ramp uptimes, hold times, ramp down times, cycles, etc.) using an array ofindividually controllable heating elements, or can additionally oralternatively be configured to thermocycle different amplificationsubstrates according to common thermocycling sequences using a singleheating element or an array of co-controlled heating elements. Thesample processing module 230 can additionally or alternatively include asecond purification module 235 configured to purify nucleic acidamplification products from amplification reagents (e.g., excessprimers, excess dNTPs, enzymes, salts, etc.). In variations, thepurification module 235 can include purification kits comprisingbuffers, alcohols (e.g., ethanol, isopropanol, etc.), pH indicators,chaotropic salts, nucleic acid binding fillers, and centrifugation. Thesample processing module 230 can, however, comprise any other suitableelements (e.g., spectrophotometric apparatus for quantitation,fluorescence modules for quantitation using fluorescent dyes that bindto nucleic acids, capillary elements for size selection, electrophoreticelements for size selection, filtration elements for size selection,quality control elements, etc).

For sequencing of amplified nucleic acids, the sample processing module230 can comprise a sequencing module 236 that operates according to oneof: sequencing-by-synthesis techniques (e.g., Illumina sequencing),capillary sequencing techniques (e.g., Sanger sequencing),pyrosequencing techniques, single-molecule real-time (SMRT) techniques,sequencing by ligation (e.g., SOLiD) techniques, reversible terminatorsequencing techniques, proton detection sequencing techniques, ionsemiconductor (e.g., Ion Torrent) sequencing techniques, nanoporesequencing techniques, electronic sequencing techniques, and any othersuitable type of sequencing technique. In specific examples, thesequencing module 236 of the sample processing module 230 can includeone or more of: an Applied Biosystems® ABI 3730 DNA Analyzer, a 454 LifeSciences® 454 FLX Titanium sequencer, an Illumina® sequencer (e.g., aGAIIx sequencer, a HiSeq sequencer, a MiSeq sequencer), a PacificBiosciences® PacBio sequencer, an Ion Torrent™ sequencer, and any othersuitable sequencer.

Elements of the sample processing module 230 can be configured tooperate in an automated manner, and in one example, the sampleprocessing module 230 comprises a laboratory automation workstation(e.g., a Biomek® Laboratory Automation Workstation) which automatessample container handling and processing by way of actuators and fluiddelivery systems governed by a control module. Alternatively the sampleprocessing module 230 can be configured to be operated at least in partby a trained technician, in order to provide manual or semi-manual formsof sample handling and processing. Furthermore, the sample processingmodule 230 can be configured to operate in a continuous-flow manner byusing fluidic devices (e.g., microfluidic devices) that enable multipleblocks of processing (e.g., sample lysing, nucleic acid extraction,nucleic acid purification, nucleic acid amplification, etc.) to beperformed on a single fluidic device. Alternatively, elements of thesample processing module 230 can be configured to operate morediscretely using different devices and/or different sample processchambers.

1.3.1 Sample Processing—Multiplex Amplification and Sequencing

In some embodiments of the method 100, sequencing of multiple targetregions of nucleic acid materials in a multiplex manner can beperformed. In particular, the method 100 can provide blocks configuredto perform multiplex amplification and sequencing whereby multiplexedreactions are preformed simultaneously, and in a substantiallynon-interacting manner (e.g., within a single process chamber) in orderto generate sufficient quantities of nucleic acid material forcharacterization and detection of the multiple target regions. Themultiplex amplification and sequencing method described furtherfunctions to account for limitations of current multiplex methods andsystems, which can be unreliable due to undesired interaction amongstprimers (e.g., creation of primer-dimers that can competitively amplifyduring sample amplification), time consuming, resource consuming (e.g.,expensive, requiring multiple separate reactions), and/or problematicdue to other limitations.

In one embodiment, as shown in FIGS. 7A and 7B, a method 300 formultiplex amplification and sequencing can comprise: generating asolution upon combination of a sample with a first substrate set havinga first primer type, associated with a first nucleic acid marker of afirst microorganism portion of the sample and isolated to the firstsubstrate set, and a second substrate set having a second primer typeassociated with a second nucleic acid marker of a second microorganismportion of the sample and isolated to the second substrate set S310;simultaneously amplifying genetic content associated with the firstnucleic acid marker by way of the first substrate set and geneticcontent associated with the second nucleic acid marker by way of thesecond substrate set in a single reaction S320; and at a sampleprocessing module within the sample handling network, generating amicrobiome sequence dataset based upon sequencing genetic contentassociated with the first and the second nucleic acid markers S330.

The method 300 is preferably performed in solution, where the primertypes and the substrate sets are not coupled to any solid matrix, andare free floating in solution. However, variations of the method 300 canbe performed wherein at least one primer type and/or substrate set isnot free-floating in solution. The method 300 is preferably implementedat least in part using an embodiment of the system 200, including thesample handling network 210 and the sample processing module 230described above; however, the method 300 can additionally oralternatively be implemented using any other suitable system.

Block S310 recites: generating a solution upon combination of a samplewith a first substrate set having a first primer type, associated with afirst nucleic acid marker of a first microorganism portion of the sampleand isolated to the first substrate set, and a second substrate sethaving a second primer type associated with a second nucleic acid markerof a second microorganism portion of the sample and isolated to thesecond substrate set. Block S310 functions to separate different primertypes associated with different nucleic acid marker targets, todifferent substrates, in order to facilitate performance of simultaneousamplification reactions in a non-interacting manner within a singleprocess chamber. As such, Block S310 can function to prevent formationof primer-dimers (e.g., interacting primers that result from the use ofprimers that are sufficiently long, but still shorter than nucleic acidfragments intended for amplification), which can competitively amplifywith target nucleic acids during sample processing. Block S310 ispreferably implemented at a variation of the sample processing moduledescribed in relation to Block S130 above; however, Block S310 canalternatively be implemented at any other suitable system configured tocombine biological samples with process reagents in a sterile anddependable manner.

In Block S310, the first primer type can include a single primer (e.g.,a forward primer, a reverse primer), or can alternatively comprise apair of primers (i.e., a forward primer and reverse primer pair).Primers of the first primer type used in Block S310 can additionallycorrespond to target 16S regions, target 18S regions, or target ITSregions of a nucleic acid strand, in order to enable characterization ofan associated first nucleic acid marker of a first microorganism portionwithin the sample. Similarly, primers of the second primer type caninclude a single primer or a pair of primers, and can be configured tocorrespond to target 16S regions, target 18S regions, or target ITSregions of a nucleic acid strand, in order to enable characterization ofan associated second nucleic acid marker of a second microorganismportion within the sample. The first primer type and the second primertype used in Block S310 preferably correspond to different nucleic acidmarkers associated with different microorganism portions within thesample, in order to enable characterization of different markers withina single amplification reaction in subsequent blocks of the method 300.Example primers of the first primer type and primers of the secondprimer type can include primers described in Tables 1 and 2, describedin the Appendix of U.S. App. No. 61/953,683, entitled “MultiplexMarkers” and filed on 14 Mar. 2014, or any other suitable primers.

In Block S310, the first substrate set type preferably comprises a solidsupport having desired physical and/or chemical properties that canfacilitate performance of multiplex reactions, or facilitate subsequentisolation of amplification products post-amplification. Substrates ofthe first substrate set type preferably have a dimension sufficientlylarge enough (e.g., greater than 10 nm) to prevent primer-primerinteractions. Additionally, substrates of the first substrate type canhave properties that allow for their manipulation (e.g., in solution),including one or more of: morphological properties (e.g., shape, size,etc.), magnetic properties (e.g., paramagnetic properties, diamagneticproperties), density properties (e.g., to affect buoyancy in solution),mass distribution properties (e.g., to affect inertial behavior),conductivity properties (e.g., thermal conductivity properties,electrical conductivity properties), electrical charge-based properties,chemical reactivity-derived properties, and any other suitable type ofproperty. As such, the ability to selectively manipulate substrates ofthe first substrate type can enhance performance of multipleamplification and sequencing reactions, with reactions occurring in anon-interacting manner. However, substrates of the first substrate settype can alternatively have any other suitable dimensions, shape,physical properties, and/or chemical properties.

In variations, the first substrate set type used in Block S310 cancomprise three dimensional substrates (e.g., beads, particles, matrices)and/or two-dimensional substrates (e.g., planar surfaces, non-planarsurfaces) coupled to functional moieties that react with portions ofdifferent primer types in a selective manner. Substrates of the firstsubstrate type can comprise one or more of: a metallic material (e.g.,gold-based material, zirconium-based material, iron-based material,platinum-based material, etc.), a ceramic material (e.g., glass,silica-based material, silicon-based material) and any other suitablematerial treated for ligation to primers of the first primer type. Assuch, after an amplification reaction, one amplicon strand remains boundto a substrate, while the complementary amplicon strand is freed intosolution.

In one variation, the first substrate set type can include beads bondedto (e.g., covalently bonded to) or comprising functional moietiesconfigured to couple to at least one primer of the first primer type. Inthis variation, each substrate of the first substrate set can have onecoupled primer or primer pair (e.g., forward primer and reverse primerpair), or can include multiple primers or primer pairs of the firstprimer type. In another variation, the first substrate set type caninclude a planar or non-planar substrate coupled to forward and reverseprimers of the first primer type, in order to enable bridge-PCR fornucleic acid strands in a sample. Alternative variations can, however,comprise any other suitable substrate type configured to couple to anysuitable number of primers of the first primer type in any othersuitable manner.

The second substrate set type used in Block S310 can be identical to thefirst substrate set type in composition, morphology, and properties, asdescribed above, aside from aspects of coupling to a different primertype. Alternatively, the second substrate set type used in Block S310can be substantially different from the first substrate set type incomposition, morphology, and/or properties, in order to enableindependent manipulation of substrates of the second substrate set typeand substrates of the first substrate set type. In one variation,substrates of the first substrate set type can have a first property(e.g., magnetic property, buoyancy-related property, size-relatedproperty, etc.) and substrates of the second substrate set type can havea second property, different from the first property, that allowssubstrates of the first substrate type and substrates of the secondsubstrate type to be manipulated independently of each other. In onesuch example, substrates of the first substrate set type can be repelledby an applied magnetic field, while substrates of the second substrateset type can be attracted by the applied magnetic field, in order toallow for physical separation of the first substrate set type (andmaterials coupled thereto) and the second substrate set type (andmaterials coupled thereto) when desired. The second substrate set typeand the first substrate set type can, however, comprise any othersuitable combination of similar or dissimilar properties.

The second substrate set type and first substrate set type used in BlockS310 can be completely isolated from each other, or can alternatively beindirectly coupled to each other, for instance, by occupying differentregions of a larger substrate. Still alternatively, the first substrateset type and the second substrate set type can be positionallyconfigured relative to each other in any other suitable manner.

While two primer types are described in relation to Block S310 above,variations of the method 300 can be expanded to cover variationsinvolving more than two primer types coupled to more than two substrateset types. Furthermore, in alternative variations, one of the differentprimer types can be uncoupled from a substrate set type (e.g., such thatthe primer type is free-floating in solution, while other primer typesare coupled to different sets of substrates).

Block S320 recites: simultaneously amplifying genetic content associatedwith the first nucleic acid marker by way of the first substrate set andgenetic content associated with the second nucleic acid marker by way ofthe second substrate set in a single reaction. Block S320 functions toenable simultaneous amplification of multiple nucleic acid regions innon-interacting reactions, and in a manner that avoids undesiredprimer-primer interactions. Block S320 is preferably performed with thesolution comprising the sample, the first substrate set having the firstprimer type, and the second substrate set having the second primer typecontained within a single process chamber, such that multiplenon-interacting amplification reactions are performed simultaneously inthe single process chamber. In one variation, properties of thesubstrate sets can be used to further prevent interaction betweenamplification reactions associated with the first nucleic acid markerand amplification reactions associated with the second nucleic acidmarker. In one such example, wherein the first substrate set is repelledby a magnetic field and wherein the second substrate set is attracted bya magnetic field, physical separation between simultaneously occurringreactions associated with a first nucleic acid marker and a secondnucleic acid marker can be enhanced by positioning a magnetic fieldproximal to the process chamber containing the solution. In another suchexample, wherein the first substrate set has a first magnetic strengthand wherein the second substrate set has a second magnetic strength,physical separation between simultaneously occurring reactionsassociated with a first nucleic acid marker and a second nucleic acidmarker can be enhanced by positioning a magnetic field proximal to theprocess chamber containing the solution. In yet another such example,wherein the first substrate set has a first density and wherein thesecond substrate set has a second density different from the firstdensity, physical separation between simultaneously occurring reactionsassociated with a first nucleic acid marker and a second nucleic acidmarker can be enabled according to density-based separation between thefirst substrate set and the second substrate set. However, simultaneousamplification of genetic content associated with the first nucleic acidmarker and genetic content associated with the second nucleic acidmarker can be performed in any other suitable manner.

In Block S320, amplification is preferably performed in a manner similarto that described in Block S35 above, whereby amplification can includeone of: polymerase chain reaction (PCR)-based techniques (e.g.,solid-phase PCR, RT-PCR, qPCR, multiplex PCR, touchdown PCR, nanoPCR,nested PCR, hot start PCR, etc.), helicase-dependent amplification(HDA), loop mediated isothermal amplification (LAMP), self-sustainedsequence replication (3SR), nucleic acid sequence based amplification(NASBA), strand displacement amplification (SDA), rolling circleamplification (RCA), ligase chain reaction (LCR), and any other suitableamplification technique. Amplification is further preferably performedusing an embodiment, variation, or example of the thermocycling module234 described in relation to Block S130 above. However, amplificationcan additionally or alternatively be performed using any other suitabletechnique and/or system.

Block S330 recites: at a sample processing module within the samplehandling network, generating a microbiome sequence dataset based uponsequencing genetic content associated with the first and the secondnucleic acid markers. Similar to the above variations and examples ofamplification, sequencing in a multiplexed, but non-interacting mannercan be performed using different properties of the first substrate setand of the second substrate set. Sequencing genetic content associatedwith the first and the second nucleic acid markers in Block S330 ispreferably performed in a manner similar to that described in Block S37above, whereby sequencing can include methods involving targetedamplicon sequencing and/or metagenomic sequencing, implementingtechniques including one or more of: sequencing-by-synthesis techniques(e.g., Illumina sequencing), capillary sequencing techniques (e.g.,Sanger sequencing), pyrosequencing techniques, single-molecule real-time(SMRT) techniques, sequencing by ligation (e.g., SOLiD) techniques,reversible terminator sequencing techniques, proton detection sequencingtechniques, ion semiconductor (e.g., Ion Torrent) sequencing techniques,nanopore sequencing techniques, electronic sequencing techniques, andany other suitable type of sequencing technique. Furthermore, sequencingis preferably performed using an embodiment, variation, or example ofthe sequencing module 236 described in relation to Block S130 above.However, sequencing in Block S330 can alternatively be performed usingany other suitable sequencing technique/system.

While multiplex markers are described in the context of microbiomecharacterization and sequencing, variations of the methods for multiplexamplification and sequencing described above can be adapted to wholegenome sequencing methods, single nucleotide polymorphism detection,screening and gene expression monitoring, and any other suitableapplications benefiting from multiplex amplification and sequencing.

1.3.1 Sample Processing—Next Generation Amplification and Sequencing

In some embodiments of the method 100, a process 700 for next generationamplification and sequencing, as shown in FIG. 8, can includesimultaneously amplifying an entire 16S region for each of a set ofmicroorganisms S710, fragmenting amplicons of the entire 16S region foreach of the set of microorganisms to generate a set of ampliconfragments S750, and generating an analysis based upon the set ofamplicon fragments S790 wherein the analysis includes at least one ofmicroorganism population characteristics, microorganism speciesidentifications, and identified target microorganism sequences.

The process 700 functions to rapidly generate libraries of microorganismgenomes (or gene sequences) that facilitate microbiome analyses at genefunction (e.g., product attributed to a specific sequence), individualsequence, individual species, and/or entire microbiome levels. Theprocess 700 can also facilitate multiplex PCR methods, single-pot PCRmethods, multiple-pot PCR methods, and/or any other suitable PCRmethods. In particular, the process 700 can facilitate processing of 16Ssequences (i.e., a relatively long target amplicon) using inexpensiveuniversal primers, while enabling robust analytical results to beobtained. In variations, the process 700 can be adapted to processingand analyzing nucleic acid regions of interest in addition to the 16Sregion. For instance, variations of the process 700 can be adapted toanalysis of heat shock proteins, antibiotic resistance genes (e.g.,aminoglycoside resistance genes, beta lactamase resistance genes,macrolide-lincosamide-streptogramin B resistance genes, multi-drugtransporter resistance genes, tetracycline resistance genes, vancomycinresistance genes, etc.), the 18S region of organisms, the ITS region oforganisms, proteins that code for specific enzymes, human genes (e.g.,as in genomic analyses), and any other suitable region of interest.

Block S710 recites: amplifying an entire 16S region for each of a set ofmicroorganisms, which functions to amplify whole regions of interest(i.e., the 16S region) of a bacterial genome. Instead of amplifying andanalyzing each subregion (e.g., the V1-V9 hypervariable subregions, theV4 subregion) of the 16S region independently, Block S710 allows foramplification of the entire 16S region of a bacterial genome, for a setof microorganisms. Downstream analysis of the hypervariable subregions(i.e., the V1-V9 subregions, the V4 subregion) can still, however, beperformed in implementation of the process 700, which allows foridentification and/or differentiation of different taxonomic groups ofmicroorganisms or specific sequences, thus providing insights into one'smicrobiome composition. In Block S710, amplification is preferablyperformed with universal primers appropriate for a wide variety ofmicroorganisms. In examples, amplification is performed with universalprimers comprising one or more of: an 8F primer, a 27F primer, a CC[F]primer, a 357F primer, a 515F primer, a 533F primer, a 16S.1100.F16primer, a 1237F primer, a 519R primer, a CD[R] primer, a 907R primer, a1391R primer, a 1492R(I) primer, a 1492R(s) primer, a U1492R primer, a928F primer, a 336R primer, an 1100F primer, an 1100R primer, a 337Fprimer, a 785F primer, an 805R primer, a 518R primer, and any othersuitable universal primer. Alternatively, for samples in which specificprimers would be appropriate, amplification can be performed withspecific primers. In examples, specific primers can include: a CYA106primer (for cyanobacteria), a CYA359F primer (for cyanobacteria), an895F primer (for bacteria excluding plastids and cyanobacteria), aCYA781R primer (for cyanobacteria), a 902R primer (for bacteriaexcluding plastids and cyanobacteria), a 904R primer (for bacteriaexcluding plastids and cyanobacteria), an 1100R primer (for bacteria),an 1185mR primer (for bacteria excluding plastids and cyanobacteria), an1185aR primer (for lichen-associated Rhizobiales), a 1381R primer (forbacteria excluding Asterochloris species plastids), or any othersuitable specific primer.

In Block S710, amplification is preferably performed for a number ofcycles to achieve a desired number amplicons (e.g., total number ofamplicons, total concentration of amplicons, total number of 16Samplicons per microorganism, etc.). In a specific example, amplificationin Block S710 can be performed for 30 cycles to achieve a desired numberof amplicons per microorganism represented in a sample. However, anyother suitable number of cycles of amplification can be performed inBlock S710. In Block S710, amplification preferably includes effectivedenaturation of a nucleic acid template, adequate extension times togenerate amplicons, and protection of target amplicons from damage(e.g., by depurination). In examples, effective denaturation can beachieved using one or more of: higher temperatures for shorter durationsand cosolvents (e.g., 1-10% DMSO, Betaine). In examples, extension canbe achieved at a temperature below 68° C. and for a duration greaterthan 15 minutes. However, any other suitable amplification conditionscan be used in Block S710.

Block S750 recites: fragmenting amplicons of the entire 16S region foreach of the set of microorganisms to generate a set of ampliconfragments, which functions to generate shorter read sequences that canbe sequenced and/or analyzed according to other blocks of the method. InBlock S750, fragmenting can be performed using one or more of: enzymaticfragmentation methods (e.g., Nextera enzyme-mediated fragmentation),bead beating, sonication (e.g., with a Covaris sonication device, with aBiruptor sonication device, etc.), and any other suitable ampliconfragmentation mechanism. In variations, fragmentation length can becontrolled based upon the intensity of the fragmentation mechanism (e.g.concentration of enzyme, intensity of bead beating, intensity ofsonication), the duration over which the fragmentation mechanism isapplied, using a combination of fragmentation mechanisms, and/or in anyother suitable manner (e.g., size of beads used in bead beating).Furthermore, in implementation of Block S750, size-selection offragments with a desired length (e.g., for sequence reads) can beperformed. In variations, size selection can be performed using one ormore of: magnetic separation (e.g., paramagnetic beads with a bindingmoiety, diamagnetic beads with a binding moiety, AMPure beads, MagJETbeads, etc.), buoyancy-based separation (e.g., low density beads with abinding moiety), microfluidic channel-based separation (e.g., usinginertial focusing, using stagnation flows, using confining channels,etc.), and any other suitable size-selection approach.

Block S790 recites: generating an analysis based upon the set ofamplicon fragments wherein the analysis includes at least one ofmicroorganism population characteristics, microorganism speciesidentifications, and identified target microorganism sequences. BlockS790 functions to further process the set of amplicon fragmentsgenerated as outputs from Block S750, and to analyze the amplicons toderive sequence-specific insights, species-specific insights, othertaxonomic group-specific insights, and/or microbiome population-specificinsights. Block S790 can include one or more of: sequencing the set ofamplicon fragments S791, assembling a full gene based upon sequencedamplicon fragments S792, performing Bayesian statistics forcharacterization based upon species, strain and/or gene identificationS793, detection of specific sequences from the set of amplicon fragmentsS794, analyzing product-sequence associations based upon reading the setof amplicon fragments S795, and performing any other suitable downstreamanalysis of the set of amplicon fragments.

In variations and examples of Block S791, sequencing the set of ampliconfragments can include any one or more of: ligating at least a subset ofthe set of amplicon fragments (e.g., using a Nextera ligation processreagent); performing an enzyme-mediated reaction (e.g., enzyme-mediatedinsertion, enzyme-mediated integration, enzyme-mediated synthesis, etc.)with amplicons of the set of amplicon fragments; combining the set ofamplicon fragments with custom primers associated with a sequencingtechnique (e.g., custom Illumina® primers for a sequencing-by-synthesisapproach); performing random primer PCR (e.g., random amplifiedpolymorphic DNA PCR); and performing any other suitable sequencingoperation, variations and examples of which are described in otherportions of this specification.

In variations and examples of Block S792 and S794, assembling a fullgene based upon sequenced amplicon fragments and/or detection ofspecific sequences from the set of amplicon fragments functions tospecific gene and/or nucleic acid sequence-level analyses associatedwith an individual's microbiome to be analyzed. Blocks S792 and/or S794can be performed as described in relation to Block S140 below, whereinsequence alignment, mapping, and encoding enable full gene assemblyand/or detection of specific sequences from the set of ampliconfragments. Additionally or alternatively, full gene assembly and/ordetection of specific sequences from the set of amplicon fragments canbe performed in any other suitable manner.

In variations and examples of Block S793, performing Bayesian statisticsfor characterization based upon species, strain and/or geneidentification functions to implement bioinformatics techniques toreveal intrinsic features (e.g., phylogenetic relationships, metabolicpotential, diversity-related features, etc.) derived from ampliconfragments of the 16S region. In Block S793, Bayesian statisticsalgorithms utilized begin with a prior probability distribution thatrepresents what is known about the diversity of the microbiomeassociated with a sample. Block S793 can implement any suitable numberof assumptions (e.g., assumptions related to interdependencies betweenspecies, assumptions related to aggregation of species, etc.) related todiversity of the microbiome. The Bayesian approach then determines aposterior distribution using observed sequence information to generateprobabilities of different estimations of microbiome populationcharacteristics. Outputs of Block S793 can be fine-tuned based uponincorporation of weighting factors (e.g., lower weights attributed tounreliability of low frequency reads), use of Bayesian inference toupdate the probability of a diversity hypothesis (i.e., as newinformation is acquired), and/or in any other suitable manner.Furthermore, outputs of Block S793 for individual microbiome communitiescan be used to generate comparisons of diversity between multiplemicrobiome communities, as described in further detail below.Additionally or alternatively, Block S793 can implement any othersuitable bioinformatics-based approach to describe species, strain,and/or gene diversity of the microbiome associated with a sample.

While Blocks S710, S750, and S790 are described in one order above,amplification, fragmentation, sequencing, and downstream processing canalternatively be performed in any other suitable order, in order tofacilitate generation of microbiome-based analyses from biologicalsamples.

Furthermore, while the process 700 is described in the context ofmicrobiome characterization and sequencing, variations of the process700 described above can be adapted to whole genome sequencing methods,single nucleotide polymorphism detection, screening and gene expressionmonitoring, and any other suitable applications benefitting frommultiplex amplification and sequencing.

1.4 Microbiome Characterization—Sequence Alignment, Mapping, andEncoding

Block S140 recites: at a processing system within the sample handlingnetwork, identifying a set of microorganisms represented in themicroorganism portion based upon performance of a mapping operation onportions of the microbiome sequence dataset. Block S140 functions toimplement computational processing techniques, in transforming an inputof unanalyzed microbiome sequence data into an output that characterizesrepresented microorganisms within the sample. Outputs of Block S140 canthus be used to derive values of parameters related to relativedistributions of microorganism groups within the microbiome of anindividual, abundances of microorganism groups within the microbiome ofan individual, represented genetic markers within the microbiome of anindividual, and/or any other suitable parameters, as further describedin Block S150 below. In variations, as shown in FIG. 9A, computationalprocessing in Block S140 can include any one or more of: identifyingsequences associated with the microorganism portion S141 (e.g., asopposed to human sequences and contaminants), and performing alignmentand mapping of sequences associated with the microorganism portion S142(e.g., alignment of fragmented sequences using one or more ofsingle-ended alignment, ungapped alignment, gapped alignment, pairing).

Identifying sequences associated with the microorganism portion, as inBlock S141, can include mapping of sequence data from sample processingto a human reference genome (e.g., provided by the Genome ReferenceConsortium), in order to remove human genome-derived sequences.Additionally, identifying sequences associated with the microorganismportion can include discarding sequences associated with unintelligibleand/or low quality reads at a module of the processing system configuredto perform quality filtering of reads (e.g., according to the use of Qor Phred quality scores), such that only non-human and high qualityreads (e.g., reads above a certain quality score threshold in terms of aQ or Phread score) remain after Block S141 is performed. However,identifying sequences associated with the microorganism portion can beperformed in any other suitable manner.

In Block S142, unidentified sequences remaining after mapping ofsequence data to the human reference genome can then be furtherclustered into operational taxonomic units (OTUs) based upon sequencesimilarity and/or reference-based approaches (e.g., using VAMPS, usingMG-RAST, using QIIME databases), assembled based upon overlapping withother reads, and aligned to reference sequences. In Block S142,alignment can be performed in multiple phases, using one or more of:single-ended alignment, ungapped alignment, gapped alignment, pairedalignment (e.g., with forward and reverse pairs of sequences), clusteredalignment (e.g., with clustering of forward reads and clustering ofreverse reads), and any other suitable phase of alignment. Furthermore,alignment algorithms implemented at a module of the processing systemcan be configured for specific read lengths or ranges of read lengths,in order to increase the efficiency of alignment processing based uponsequence lengths. Alignment algorithms in Block S142 can implement ahashing approach with large contiguous seeds and/or with adaptivestopping techniques, whereby a read is considered to be aligned basedupon a determination of the best read alignment across a set of readalignment candidates, and the number of read alignment candidatesconsidered. Alignment algorithms in Block S142 can additionally oralternatively include string comparison algorithms that compare a numberof mismatches between two strings (e.g., a reference read and a sequenceread) of the same length. Alignment algorithms in Block S142 canadditionally or alternatively use profile stochastic context-freegrammars (e.g., implementing covariance models), using, for instance, anSSU-align algorithm. Any other suitable type of alignment algorithm canbe used, and variations of alignment algorithms are noted below.

In variations, alignment and mapping to reference bacterial genomes(e.g., provided by the National Center for Biotechnology Information) inBlock S142 can be performed using an alignment algorithm including oneor more of: a Needleman-Wunsch algorithm that performs a globalalignment of two reads (e.g., a sequencing read and a reference read)with a stopping condition based upon scoring of the global alignment(e.g., in terms of insertions, deletions, matches, mismatches); aSmith-waterman algorithm that performs a local alignment of two reads(e.g., a sequencing read and a reference read) with scoring of the localalignment (e.g., in terms of insertions, deletions, matches,mismatches); a Basic Local Alignment Search Tool (BLAST) that identifiesregions of local similarity between sequences (e.g., a sequencing readand a reference read); a FPGA accelerated alignment tool; a BWT-indexingwith BWA tool; a BWT-indexing with SOAP tool; a BWT-indexing with Bowtietool; Sequence Search and Alignment by Hashing Algorithm (SSAHA2) thatmaps nucleic acid sequencing reads onto a genomic reference sequenceusing word hashing and dynamic programming; and any other suitablealignment algorithm. Mapping of unidentified sequences in Block S142 canfurther include mapping to reference viral genomes and/or fungalgenomes, in order to further identify viral and/or fungal components ofthe microbiome of an individual. For instance, PCR can be performed withmultiple markers (e.g., a first marker, a second marker, a third marker,an Nth marker) in parallel or in series, and associated with one or moreof bacterial markers, fungal markers, and eukaryotic markers.Furthermore, overlapping reads (e.g., generated by paired endsequencing) can be assembled based upon outputs of the alignmentalgorithm, or aligned sequence reads can be merged with referencesequences (e.g., using a hidden Markov model banding technique, using aDurbin-Holmes technique). Alignment and mapping in Block S142 can,however, implement any other suitable algorithm or technique.

In relation to Blocks S140, S141, and S142, sequence reads can beencoded to facilitate alignment and mapping operations performed. In oneexample, each base of a sequence can be encoded as a byte according tothe arrangement 0000TGCA, whereby the least significant bit is 1 if thebase is sequenced as possibly containing the base A (e.g., A isrepresented as 00000001), the next significant bit is 1 if the base issequenced as possibly containing the base C (e.g., C is represented as00000010), the next significant bit is 1 if the base is sequenced aspossibly containing the base G (e.g., G is represented as 00000100), andthe next significant bit is 1 if the base is sequenced as possiblycontaining the base T (e.g., T is represented as 00001000). In theexample, the four most significant bits are set to zero. However,alternative variations of the example can encode bases in any othersuitable manner. Furthermore, known sequences of primers used duringamplification in Block S130 can be used to trim sequence reads to omitprimer sequences to increase the efficiency of alignment and mapping.

In one variation with encoded sequences, a simhash (i.e., fuzzy hash)algorithm can be used to form aligned clusters that can be compared toreference sequences in an efficient manner. In this variation, thesimhash algorithm can be configured to ignore the four most significantbits set to zero (e.g., in relation to the example of encoding describedabove), and to produce a hash, wherein similar inputs are converted tosimilar hash outputs in a manner that facilitates cluster analyses ofhashed outputs. The simhash algorithm can be configured with acomparison sequence length (e.g., having a given “wordlength”) in orderto determine how sensitive the hash is to ordering, which can be used todetermine the granularity of the algorithm and the number of resultingclusters.

Hashing can include reducing a length of a read to a shorter length(e.g., from 300 bases to 10-25 bases) in a fuzzy hash process, and usingthe fuzzy hash process to cluster sequences with identical fuzzy hashes.The distribution of clustered sequences can comprise a large group ofclusters with a small number of reads (e.g., 1-5 reads), which can beprocessed separately from a group of clusters with a large number ofreads. After the sequences are clustered together, they can be indexedwith a strict hash (e.g., a word length of 25-300 bases), and theclusters can be compared to a set of reference sequences, wherein theset of reference sequences can be trimmed (e.g., based upon known primersequences used to amplify the sample) and hashed at the same hash lengthas that of the clusters to produce hashed references that are associatedwith the set of reference sequences. Then, further hashing of both theset of reference sequences and the distribution of clustered sequences,with comparison between the set of reference sequences and thedistribution of clustered sequences at each iteration, can be performeduntil a threshold condition of matching between reference sequences andclustered sequences is satisfied.

In a first variation, the hashing process can be performed for ampliconsof similar type (e.g., amplicons of specific 16S hypervariablesubregions, amplicons of 18S subregions, amplicons of ITS subregions,etc.), whereby clusters of amplicon reads having a desired length can beindexed and compared to one or more reference sequences (e.g., referencesequences trimmed to the desired length). In the comparison operation,the amplicon reads and the reference reads can each be encoded as a byte(e.g., as a byte according to the arrangement 0000TGCA, as describedabove), whereby each base of a read is aligned and the sum of thealigned encoded bases is used for comparison according to a thresholdcondition. In one example, as shown in FIG. 16, ones in an encoded basecan be transformed into twos and zeroes in an encoded base can betransformed into ones prior to summation, and the summed amplicon readcan then be transformed back into binary, whereby positive digits aretransformed back to ones, and negative digits are transformed back tozeroes. Summation and comparison can, however, be performed in any othersuitable manner. In the first variation, amplicon reads can then begrouped by similarity according to the threshold condition, in order tofacilitate generation of microbiome population insights (e.g., taxonomicgroup representation, diversity, etc.).

In a second variation, the hashing process can be performed for a set ofrandom amplicon fragments (e.g., generated according to the process 700described above), whereby a desired word length (e.g., 1-5 bases) can beused for comparison between amplicon fragment reads and reference reads.In the second variation, fragments can be clustered according tofragment length or any other suitable characteristic. In the secondvariation, a sequence (e.g., GCCA) can be chosen and detected (or notdetected) across all amplicon fragment reads, wherein the chosensequence can be used to compare the amplicon fragment reads to thereference read. As such, the second variation can provide anorder-independent comparison operation that is sensitive to deletions inbases of a sequence. Similar to the first variation, in the comparisonoperation, the random amplicon fragment reads and the reference readscan each be encoded as a byte (e.g., as a byte according to thearrangement 0000TGCA, as described above), whereby each base of a readis aligned and the sum of the aligned encoded bases is used forcomparison according to a threshold condition. Summation and comparisoncan, however, be performed in any other suitable manner. In the secondvariation, reads can then be grouped by similarity according to thethreshold condition, in order to facilitate generation of microbiomepopulation insights (e.g., taxonomic group representation, diversity,etc.).

Mapping of encoded sequences to reference sequences can, however, beperformed in any other suitable manner.

As noted above, Block S140 is preferably implemented by way of a system200, as shown in FIGS. 2 and 9B, that includes a processing system 240configured to perform microbiome-based analyses on sequenced nucleicacid content of biological samples processed within the sample handlingnetwork 210. The processing system 240 can be in direct communicationwith modules of the sample processing module 230, and in one variation,a sequencing module 236 of the sample handling network 210 can beconfigured to provide sequenced data as an output to a module of theprocessing system 240. Additionally or alternatively, the processingsystem 240 can be configured to receive inputs from outputs of thesample processing module 230 by way of a storage device 241 configuredto store derived from processing of samples received at the samplehandling network 210. The processing system 240 is preferablyimplemented in one or more computing systems, wherein the computingsystem(s) can be implemented at least in part in the cloud and/or as amachine (e.g., computing machine, server, etc.) configured to receive acomputer-readable medium storing computer-readable instructions. Assuch, the processing system 240 can comprise one or more processingmodules, implemented in the cloud and/or as machine, comprisinginstructions for performing blocks of the method 100. In one variation,the processing system 240 can include a first module 242 configured toreceive data derived from outputs of the sequencing module 236, a secondmodule 243 configured align and map sequenced data from the first module242 as described in relation to Blocks S140-S142 above, and a thirdmodule 244 configured to receive outputs of the second module 243 inorder to generate features and derive insights, as described in relationto Block S150 below. The processing system 240 can, however, beconfigured in any other suitable manner.

1.4.1 Processing and Characterization Controls—Sample Identification

In processing a sample to generate a microbiome sequence dataset from asample, Blocks S130 and/or S140 can include an identification step thatcombines one or more nucleic acid identification sequences as “barcodes”with each sample or for each individual associated with a set of samplesreceived at the sample handling network in Block S120. Use ofidentification sequences can thus function to enable identification ofsamples in association with a specific individual, enable detection ofcontamination (e.g., cross-contamination) of samples, and facilitatequantification of reads associated with given sequences in a sample thatis processed in a multiplex manner. A nucleic acid identificationsequence can comprise a synthetic strand of one or more of 16S DNA, 16SRNA, 18S DNA, 18S RNA, ITS DNA, ITS RNA, and any other suitable regionof DNA or RNA, wherein synthetic nucleic acid molecules can benon-naturally occurring and/or comprise non-natural bases.Alternatively, a nucleic acid identification sequence can comprise anon-synthetic strand of nucleic acid material.

Furthermore, an identification sequence can be used for identificationbased upon its specific sequence and/or its expression level insolution. With multiple nucleic acid identification sequences andmultiple expression levels for each sequence, m^(N) samples can beuniquely encoded, where N represents the number of unique nucleic acididentification sequences and m represents the number of uniqueexpression levels for each unique nucleic acid identification sequence.In a specific example, 10 distinct nucleic acid identificationsequences, each having three possible expression levels (e.g., noexpression, moderate expression, high expression) provides encoding forup to 3¹⁰ samples. However, any other suitable number of identificationsequences, and any other suitable number of expression levels can beused to expand the total number of possible encoded samples. Inimplementing nucleic acid barcodes, Blocks S130 and/or S140 can thusinclude generating a mixture upon combination of an identifying reagent,including a subset of a set of nucleic acid identification sequences,each having one of a set of expression levels, with a sample receivedfrom an individual, whereby later detection of the nucleic acididentification sequences and expression levels can be used to uniquelyidentify the sample at various stages of sample processing. Theidentifying reagent can be included in a sample container provided in asampling kit, as described in relation to Block S100 above, or canadditionally or alternatively be combined with a sample after a samplehas been received at the sample handling network.

One variation of a method 400 for sample processing using identificationsequences, as shown in FIG. 10, can include: generating a mixture uponcombining a nucleic acid sample, generated from a sample, with a firstsynthetic nucleic acid molecule having a first sequence and a firstconcentration and a second synthetic nucleic acid molecule having asecond sequence and a second concentration S41; generating a sequencedataset based upon sequencing nucleic acid content of the microbiome andof the first and the second synthetic nucleic acid molecule of themixture S42; and associating the sequence dataset with the individualbased upon identification of the first and the second sequence and thefirst and the second concentration from the sequence dataset S43. BlocksS41-S43 can, however, be expanded to cover variations with fewer than ormore than two synthetic acid molecules, each with a range of expressionlevels, functioning as “barcode” or identification sequences.

Block S41 recites: generating a mixture upon combining the nucleic acidsample with a first synthetic nucleic acid molecule having a firstsequence and a first concentration and a second synthetic nucleic acidmolecule having a second sequence and a second concentration. Block S41functions to tag each sample received in Block S120 with an identifyingreagent having a specific and known composition of one or moreidentification sequences, which can be detected and used for sampleidentification during other blocks of the method 100. Generating themixture in Block S43 can be performed during sample provision andfacilitated by way of sample containers of the sampling kit provided inBlock S110. In one variation, each sample container configured toreceive a sample in Block S100 can be packaged with the identifyingreagent having the first and the second synthetic nucleic acidmolecules, such that the identifying reagent is combined with the sampleas the individual (or another entity) mixes (e.g., stirs, shakes) thesample container during sample pre-processing. In this variation,sampling kits can be linked with specific identifying reagents, in orderto enable association of samples received by way of the sampling kits,with the synthetic nucleic acid sequences of the identifying reagent.Alternatively, identifying reagent(s) having the first and the secondsynthetic nucleic acid molecules can be combined with the sample afterreception at the sample handling network, in order to generate themixture.

The barcode sequences can comprise greater than 5 bases, but canalternatively comprise any other suitable number of bases. Furthermore,the barcode sequences and concentrations are preferably different fromthat contributed by potential undesirable sample contaminants, such thatconfusion between contaminants and barcode sequences is avoided. Evenfurther, the barcode sequences can comprise sequences substantiallydifferent from target nucleic acid sequences of the sample used formicrobiome characterization, which can facilitate making distinctionsbetween target nucleic acid sequences and barcode sequences duringsample processing. Alternatively, the barcode sequences can comprisesequences similar to target nucleic acid sequences of the sample usedfor microbiome characterization, with any suitable degree of similarity.The first concentration of the first synthetic nucleic acid molecule andthe second concentration of the second synthetic nucleic acid moleculeare preferably selected amongst a discrete number of concentrations(e.g., up to 10 concentrations ranging between a low concentration and ahigh concentration); however, first concentration of the first syntheticnucleic acid molecule and the second concentration of the secondsynthetic nucleic acid molecule can alternatively be selected amongst acontinuous spectrum of concentrations. Furthermore, identifyingcharacteristics of the first synthetic nucleic acid molecule and thesecond synthetic nucleic acid molecule can comprise characteristicsdiffering in more than sequence and concentration (e.g., difference inlength, difference in morphology, difference in folding behavior, etc.).

As noted above, the barcode sequences can be associated with primersimplemented during an amplification process, or otherwise combined witha sample in any other suitable manner. Example barcode sequences arenoted in Tables 3 and 4; however, variations and examples of Block S41can include any other suitable barcode sequences.

Block S42 recites: generating a sequence dataset based upon sequencingnucleic acid content of the microorganism ecosystem and of the first andthe second synthetic nucleic acid molecule of the mixture, whichfunctions to sequence nucleic acid content of the sample for microbiomecharacterization, in cooperation with sequencing of the first and thesecond synthetic nucleic acid molecules for sample identification. BlockS42 is preferably implemented at an embodiment, variation, or example ofthe sample processing module described in relation to Block S130 above;however, Block S42 can additionally or alternatively be implemented atany other suitable system configured to amplify and/or sequence nucleicacid content of a biological sample. In Block S42, amplification andsequencing are preferably performed according to the embodiments,variations, and/or examples of Blocks S130, S35, and S37 describedabove; however, amplification and sequencing in Block S42 canalternatively be performed in any other suitable manner.

Block S43 recites: associating the sequence dataset with the individualbased upon identification of the first and the second sequence and thefirst and the second concentration from the sequence dataset, whichfunctions to verify the identity of a sample and/or sequence datasetbased upon detection and characterization parameters derived from thefirst synthetic nucleic acid molecule and the second synthetic nucleicacid molecule upon processing as in Block S42. Block S43 is preferablyperformed at an embodiment, variation, or example of the processingsystem described in relation to Blocks S140-S142 above; however BlockS43 can additionally or alternatively be implemented using any othersuitable computing system configured to determine parameters derivedfrom sequencing data for purposes of sample identification.

In Block S43, the processing system can be configured to locate allreads corresponding to the first and the second sequence, as associatedwith the first synthetic nucleic acid molecule and the second syntheticnucleic acid molecule. The processing system can then be configured todetermine a first value indicative of a first abundance of the firstsynthetic nucleic acid molecule and a second value indicative of asecond abundance of the second synthetic nucleic acid molecule. Thefirst value and the second value can then be used to estimate ordetermine a value of a parameter indicative of the first concentrationand the second concentration of the first and the second syntheticnucleic acid molecules, in order to verify identification of thesample's identity based upon barcode sequences. The parameter can be aratio between the relative abundances of reads having the first sequenceand reads having the second sequence, which can be indicative of a ratiobetween the first concentration and the second concentration.Alternatively, the parameter can be related to the first and/or thesecond concentration, as adjusted by an efficiency of primers used inthe amplification process. In variations, the first value and the secondvalue can be determined according to quantitation of the first and thesecond synthetic nucleic acid molecules, for instance, using aspectrophotometric or fluorescence-based approach; however, the firstvalue and the second value can alternatively be determined in any othersuitable manner.

In Block S43, the processing system can further comprise a moduleconfigured to compare reads against all synthetic nucleic acid modulesused as barcode sequences in the method 100 and/or system 200, whichfunctions to enable identification of cross-contamination betweensamples. For instance, the module can be configured to detect presenceof one or more unanticipated synthetic nucleic acid sequences present inthe sample or processed versions thereof, which can indicate thatsamples were mixed together and should not be trusted for accuratecharacterization. Upon identification of an unanticipated presence of aset of undesired synthetic nucleic acid molecules in a sample, Block S43can further include identifying a second sample associated with the setof undesired synthetic nucleic acid molecules, and performing an errorcorrection action. In variations, the error correction action cancomprise one or more of: analyzing the second sample to determine ifcontamination only occurred in one direction (e.g., the second samplecontaminated the sample, but the sample did not contaminate the secondsample) or in both directions, notifying an entity of the samplehandling network of potential contamination, notifying an entity of thesample handling network that further processing of a contaminated sampleshould not continue, notifying the individual providing the sample thatanother sample may need to be re-provided, and any other suitable errorcorrection action. Block S43 can, however, comprise any other suitablesteps or blocks configured to enhance sample identification and/oridentification of sample contamination.

While identification in Blocks S41-S43 is described in relation toanalysis of a microbiome portion of a sample from an individual, BlocksS41-S43 can be adapted to methods for performing analyses on any othersuitable biological sample, using any other suitable biologicalcomponent as a barcode/identifying feature (e.g., distribution ofsynthetic organelles for identification purposes, distribution of cellpopulations for identification purposes, etc.).

1.4.2 Processing and Characterization Controls—Plasmid Controls

In processing a sample to generate a microbiome sequence dataset from asample, Blocks S130 and/or S140 can additionally include blocksconfigured to facilitate simultaneous quantification of nucleic acidmaterial within a sample and identification of a sample in associationwith an individual. Blocks associated with simultaneous quantificationand identification can include processing a sample with a combination ofa solution having a target nucleic acid sequence and a solution having areference sequence coupled to the target sequence, which can be used toback-calculate a quantity of nucleic acid molecules having the targetsequence, while enabling verification of the identity of the sample byway of the reference sequence.

In one such variation, as shown in FIGS. 11A and 11B, a method 500 forassociating a sequence dataset with an individual and determining aquantity of nucleic acid molecules represented in the sequence datasetand having a target sequence, can include: preparing a first solutionincluding a first sample of nucleic acid material having a targetsequence S51; preparing a second solution containing a second sample ofnucleic acid material having the target sequence and an identificationsequence S52; preparing a third solution upon combination of a firstportion of the first solution and a second portion of the secondsolution, wherein the second portion includes a reference quantity ofnucleic acid material S53; preparing a fourth solution upon amplifyingnucleic acid material of the third solution S54; generating the sequencedataset based upon sequencing nucleic acid material of the fourthsolution S55; from the sequence dataset, determining a reference numberof reads associated with the identification sequence and a total numberof reads associated with the target sequence S56; determining thequantity of nucleic acid molecules having the target sequence based uponthe total number of reads, the reference number of reads, and thereference quantity of nucleic acid material S57; and associating thesequence dataset with the individual based upon at least one ofdetection of the identification sequence and the reference number ofreads S58.

The method 500 can be used to identify and quantify samples usingcombinations of synthetic nucleic acid molecules, measure backgroundcontamination to allow for quality control, enable contamination levelnucleic acid molecules to be distinguished from target nucleic acidmolecules in a sample, enable quantification of gene expression, enablesimultaneous investigation of gene expression of multiple regions withina single sample, enable relative abundances of various genetic markersto be determined, and to enable absolute abundances of certain geneticmarkers to be determined. The method 500 is preferably implemented usingan embodiment, variation, or example of the system 200, comprising asample handling module 230 and a processing system 240, described above;however, the method 500 can additionally or alternatively be implementedusing any other suitable system(s).

Block S51 recites: preparing a first solution including a first sampleof nucleic acid material having a target sequence, which functions toprovide a sample solution that can be combined with other functionalsolutions, amplified, sequenced, and analyzed in order to back-calculatea number of strands of nucleic acid molecules having the target sequencein the first sample. Preferably, the first sample comprises a nucleicacid material derived from a biological sample from an individual. Assuch, the first sample can comprise a sample taken from a collectionsite of an individual, as described in relation to Block S100 above. Thefirst solution comprising the first sample can, however, comprise anyother suitable sample having a target sequence of interest. The targetsequence is preferably a known sequence, in order to facilitatecalculation of a number of strands of nucleic acids having the targetsequence post amplification of a solution containing the samplesolution.

In one example, the target sequence can correspond to a DNA primer, suchthat the primer includes a first primer solution with a degenerate DNAsequence including the following bases: CCAGCASCYGCGGTAATTCC, and asecond primer solution with a degenerate DNA sequence including thefollowing bases: ACTTTCGTTCTTGATYRA. In another example, the targetsequence can correspond to a DNA primer, such that the primer includes afirst primer solution with a DNA sequence including the following bases:TGGTCATTTAGAGGAAGTAA, and a second primer solution with a DNA sequenceincluding the following bases: TGCGTTCTTCATCGATGC. In yet anotherexample, the target sequence can correspond to a DNA primer, such thatthe primer includes a first primer solution with a degenerate DNAsequence including the following bases: GTGCCAGCMGCCGCGGTAA, and asecond primer solution with a degenerate DNA sequence including thefollowing bases: GGACTACHVGGGTWTCTAAT. In yet another example, thetarget sequence can correspond to a DNA primer, such that the primerincludes a first primer solution with a DNA sequence including thefollowing bases: AGAGTTTGATCCTGGCTCAG, and a second primer solution witha DNA sequence including the following bases: ATTACCGCGGCTGCTGG. Thetarget sequence of the first sample can, however, comprise any othersuitable sequence corresponding to any other suitable primer(s).

Block S52 recites: preparing a second solution containing a secondsample of nucleic acid material having the target sequence and areference sequence, which functions to provide a second solution thatincludes nucleic acid molecules having features that can 1) facilitateidentification of a solution, having nucleic acid molecules with thetarget sequence, combined with the second solution upon amplificationand sequencing, and 2) quantification of nucleic acid molecules of thesolution having the target sequence. Preferably, the second samplecomprises a sample of nucleic acid material having a reference sequencethat functions as an identification sequence (e.g., a barcode, as inBlocks S41-S43 above). Furthermore, the sample of nucleic acid materialcan have a first primer part and a second primer part, associated withthe target sequence of the first solution, wherein the first primer partand the second primer part flank the identification sequence. Thereference sequence/identification sequence preferably includes syntheticnucleic acid material statistically unlikely to appear in the firstsolution with the first sample, such that the reference sequence isreadily distinguishable from sequences potentially represented in thefirst solution. However, the reference sequence/identification sequencecan alternatively be similar to a nucleic acid sequence potentiallypresent in the first solution, with any suitable degree of similarity.

In one example, the second sample of nucleic acid material having thetarget sequence and a reference sequence can include a first primer partwith a DNA sequence including the following bases: CCAGCAGCTGCGGTAATTC,followed by a reference sequence including the following bases:TACGACGGTACACGT, followed by the reverse compliment of a second primerpart including the following bases: TCGATCAAGAACGAAAGT. In anotherexample, the second sample of nucleic acid material having the targetsequence and a reference sequence can include a first primer part with aDNA sequence including the following bases: TGGTCATTTAGAGGAAGTAA,followed by a reference sequence including the following bases:TCCGAAAGGGCTTTGA, followed by the reverse compliment of a second primerpart including the following base pairs: GCATCGATGAAGAACGCA. In stillanother example, the second sample of nucleic acid material having thetarget sequence and a reference sequence can include a first primer partwith a DNA sequence including the following bases: GTGCCAGCAGCCGCGGTAA,followed by a reference sequence including the following bases:CTTATTACCTGCGAGT, followed by the reverse compliment of a second primerpart including the following base pairs: ATTAGATACCCGTGTAGTCC. In stillanother example, the second sample of nucleic acid material having thetarget sequence and a reference sequence can include a first primer partwith a DNA sequence including the following bases: AGAGTTTGATCCTGGCTCAG,followed by a reference sequence including the following bases:ACCCGTACTTCTAGT, followed by the reverse compliment of a second primerpart including the following base pairs: CCAGCAGCCGCGGTAAT. Invariations of the examples, the nucleic acid material of the secondsample can additionally or alternatively comprise RNA material.Furthermore, additional example barcode sequences are presented in Table3; however, Block S52 of the method 500 can additionally oralternatively include any other suitable barcode sequences configuredrelative to primer sequences in any other suitable manner.

Block S53 recites: preparing a third solution upon combination of afirst portion of the first solution and a second portion of the secondsolution, wherein the second portion includes a reference quantity ofnucleic acid material. Block S53 functions to create a combined solutionthat can be amplified, sequenced, and analyzed to determine a quantityof nucleic acid molecules having the target sequence in the firstsolution, as in Block S57 below. Combination can include a pipettingtechnique to combine the first portion of the first solution and thesecond portion of the second solution in a précises precise manner thatenables determination of the reference quantity of nucleic acid materialhaving the target sequence and the reference sequence; however,combination can additionally or alternatively include any other suitablemethod of sample solution combination. In Block S53, the referencequantity of nucleic acid material is preferably known, and functions tofacilitate normalization of a number of reads from part of the firstsolution, in order to enable determination of a quantity of nucleic acidmolecules having the target sequence in the first solution. Block S53 ispreferably implemented at an embodiment, variation, or example of thesample processing module 230 of the system 200 described in relation toBlock S130 above; however, Block S53 can additionally or alternativelybe implemented using any other suitable system.

Block S54 recites: preparing a fourth solution upon amplifying nucleicacid material of the third solution, which functions to facilitatesequencing in Block S54 by providing a sufficient quantity of nucleicacid material from the third solution for sequencing. Block S54 ispreferably implemented at an embodiment, variation, or example of thesample processing module described in relation to Block S130 above;however, Block S54 can additionally or alternatively be implemented atany other suitable system configured to amplify and/or sequence nucleicacid content of a biological sample. In Block S54, amplification ispreferably performed according to the embodiments, variations, and/orexamples of Blocks S130 and S35 described above; however, amplificationin Block S54 can alternatively be performed in any other suitablemanner.

Block S55 recites: generating the sequence dataset based upon sequencingnucleic acid material of the fourth solution, which functions toidentify sequences of nucleic acid material amplified in Block S54, inorder to facilitate determination of values of parameters based uponspecific sequences that can be used to determine a quantity of nucleicacid materials having the target sequence in the first solution. BlockS55 is preferably implemented at an embodiment, variation, or example ofthe sample processing module described in relation to Block S130 above;however, Block S55 can additionally or alternatively be implemented atany other suitable system configured to amplify and/or sequence nucleicacid content of a biological sample. In Block S55, sequencing ispreferably performed according to the embodiments, variations, and/orexamples of Blocks S130 and S37 described above; however, sequencing inBlock S55 can alternatively be performed in any other suitable manner.

Block S56 recites: from the sequence dataset, determining a referencenumber of reads associated with the reference sequence and a totalnumber of reads associated with the target sequence, which functions todetermine values of read parameters that can be used to determine thequantity of nucleic acid molecules having the target sequence in thefirst solution, as in Block S57. Quantification of sequence readsassociated with the reference sequence and sequence reads associatedwith the target sequence is preferably performed at an embodiment,variation, or example of the processing system 240 of the system 200described in relation to Block S140 above; however, quantification inBlock S56 can additionally or alternatively be performed at any othersuitable system configured to identify similar or identical sequencereads, compare the sequence reads to reference sequences and targetsequences, and quantify reads associated with the reference sequence andsequence reads associated with the target sequence.

Block S57 recites: determining the quantity of nucleic acid moleculeshaving the target sequence based upon the total number of reads, thereference number of reads, and the reference quantity of nucleic acidmaterial. Block S57 functions to take read counts determined in BlockS56 and the reference quantity of nucleic acid material known from BlockS53, to determine a quantity of nucleic acid molecules having the targetsequence in the first solution, based upon a back-calculation method. Inone variation of Block S57, the quantity of nucleic acid moleculeshaving the target sequence in the first solution can be determined basedupon calculation of a difference between the total number of reads andthe reference number of reads, wherein the difference is multiplied by aratio between the reference quantity of nucleic acid material and thereference number of reads. As such, in the example, the quantity ofnucleic acid molecules having the target sequence, y, can be determinedaccording to expression [1], where b is the total number of reads, wherex is the reference quantity of nucleic acid material of Block S53, andwhere a is the reference number of reads:y=(b−a)*(x/a)  [1]In Block S57, the quantity of nucleic acid molecules having the targetsequence in the first solution can, however, be determined in any othersuitable manner based upon the total number of reads, the referencenumber of reads, and the reference quantity of nucleic acid material.

Blocks S51-S57 can be further adapted to variations wherein multipletarget sequences are of interest. For instance, for a given targetsequence n, the quantity of nucleic acid molecules having the targetsequence, y_(n), can be determined according to expression [2], whereb_(n) is the total number of reads, where x_(n) is a reference quantityof nucleic acid material having the target sequence coupled with areference sequence, and where a_(n) is the reference number of readshaving the reference sequence, post amplification and sequencing:y _(n)=(b _(n) −a _(n))*(x _(n) /a _(n))  [2]

With multiple target sequences, relative abundances of nucleic acidmolecules having the respective target sequences can be determined byrelating versions of expression [2], determined for each targetsequence, to each other. In one such example applied to a first targetsequence and a second target sequence, a relative abundance betweennucleic acid molecules having the first target sequence, y₁, and nucleicacid molecules having the second target sequence, y₂, can be determinedaccording to expression [3], where b₁ is the total number of readshaving a first reference sequence post amplification and sequencing,where b₂ is the total number of reads having a second reference sequencepost amplification and sequencing, where x₁ is a reference quantity ofnucleic acid material having the first target sequence coupled with thefirst reference sequence, where x₂ is a reference quantity of nucleicacid material having the second target sequence coupled with the secondreference sequence, where a₁ is the reference number of reads having thefirst reference sequence, post amplification and sequencing, and wherea₂ is the reference number of reads having the first reference sequence,post amplification and sequencing:y ₁ /y ₂=[(b ₁ −a ₁)/(b ₂ −a ₂)]*(x ₁ /x ₂)*(a ₂ /a ₁)  [3]In expression [3], if the total number of reads having the firstreference sequence is identical to the total number of reads having thesecond reference sequence, and if the reference quantity of nucleic acidmaterial having the first target sequence coupled with the firstreference sequence is equal to the reference quantity of nucleic acidmaterial having the second target sequence coupled with the secondreference sequence, expression [3] can be simplified as expression [4]in order to facilitate determination of the relative abundances betweennucleic acid molecules having the first target sequence, y₁, and nucleicacid molecules having the second target sequence, y₂:y ₁ /y ₂=[(b−a ₁)/(b−a ₂)]*(a ₂ /a ₁)  [4]Determination of relative abundances of nucleic acid molecules havingtarget sequences can, however, be determined in any other suitablemanner according to expanded variations of Block S57.

Block S58 recites: associating the sequence dataset with the individualbased upon the reference number of reads, which functions to verify theidentity of a sample and/or sequence dataset based upon detection andcharacterization parameters derived from the reference number of readsdetermined in Block S56. Block S58 is preferably performed at anembodiment, variation, or example of the processing system described inrelation to Block S140 above; however Block S58 can additionally oralternatively be implemented using any other suitable computing systemconfigured to determine parameters derived from sequencing data forpurposes of sample identification.

Similar to Block S43 described above, the processing system implementingBlock S58 can further comprise a module configured to compare thereference number of reads against all synthetic nucleic acid modulesused as identification sequences in the method 100 and/or system 200,which functions to enable identification of cross-contamination betweensamples. For instance, the module can be configured to detect presenceof one or more unanticipated synthetic nucleic acid sequences present inthe first solution or processed versions thereof (e.g., as determinedpost-amplification and post-sequencing), which can indicate that sampleswere mixed together and should not be trusted for accuratecharacterization. Upon identification of an unanticipated presence of anunanticipated synthetic nucleic acid molecule in the first solution,Block S58 can further include identifying another sample associated withthe unanticipated synthetic nucleic acid molecule, and performing anerror correction action. In variations, the error correction action cancomprise one or more of: analyzing the other sample to determine ifcontamination only occurred in one direction (e.g., the other samplecontaminated the first sample, but the first sample did not contaminatethe other sample) or in both directions, notifying an entity of thesample handling network of potential contamination, notifying an entityof the sample handling network that further processing of a contaminatedsample should not continue, notifying the individual providing the firstsample that an additional sample may need to be re-provided, and anyother suitable error correction action. Block S58 can, however, compriseany other suitable steps or blocks configured to enhance sampleidentification and/or identification of sample contamination.

While processing and identification in Blocks S51-S58 are described inrelation to analysis of a microbiome portion of a sample from anindividual, Blocks S51-S58 can be adapted to methods for performinganalyses on any other suitable biological sample, using any othersuitable biological component that can detected and/or quantifiedthroughout processing as a barcode/identifying feature (e.g.,distribution of synthetic organelles for identification purposes,distribution of cell populations for identification purposes, etc.).

1.5 Insight Generation and Sharing

Block S150 recites: at the processing system, generating an analysisbased upon a set of features related to the microorganism portion, whichfunctions to transform outputs of Block S140 into features that can beprocessed algorithmically to determine microbiome-based insights at theindividual level and population of individuals level. As shown in FIG.12, Block S150 can include generating features derived fromcompositional aspects of the microbiome associated with the sample S151,and generating an analysis based upon features derived fromcompositional aspects of the microbiome associated with the sample S152.Blocks S150-S152 are preferably implemented at least in part at anembodiment, variation, or example of the processing system 240 of thesystem 200 described in relation to Block S140 above; however, BlocksS150-S152 can additionally or alternatively be implemented using anyother suitable system(s).

Upon identification of represented groups of microorganisms of themicrobiome associated with a sample, based upon the mapping andalignment operations of Block S140, generating features derived fromcompositional aspects of the microbiome associated with a sample can beperformed in Block S151. In one variation, generating features caninclude generating features that describe the presence or absence ofcertain taxonomic groups of microorganisms. Additionally oralternatively, generating features can include inferring phylogenetictraits associated with aligned, mapped, and/or merged reads, which caninclude determining placement of sequences on a reference phylogenetictree of microorganisms. Additionally or alternatively, generatingfeatures can include generating features describing quantities ofrepresented taxonomic groups. Additionally or alternatively, generatingfeatures can include generating features describing diversity ofdifferent microorganism groups and relative abundance of differentmicroorganism groups, for instance, using a Genome Relative Abundanceand Average size (GAAS) approach and/or a Genome Relative Abundanceusing Mixture Model theory (GRAMMy) approach that usessequence-similarity data to perform a maximum likelihood estimation ofthe relative abundance of one or more groups of microorganisms.Additionally or alternatively, generating features can includegenerating statistical measures of taxonomic variation, as derived fromabundance metrics. Additionally or alternatively, generating featurescan include generation of qualitative features describing presence ofone or more taxonomic groups, in isolation and/or in combination.Additionally or alternatively, generating features can includegeneration of features related to genetic markers (e.g., representative16S, 18S, and/or ITS sequences) characterizing microorganisms of themicrobiome associated with a biological sample. Block S120 can, however,include generation of any other suitable feature(s) derived fromsequencing and mapping of nucleic acids of a biological sample.

Upon feature generation in Block S151, generating an analysis based uponthe generated features can be performed in Block S152. In generation ofthe analysis, Block S152 can implement supplementary data that canenhance correlations and/or predictions included in the analysis. Assuch, Block S152 can include Block S153, which recites: receiving asupplementary dataset that includes demographic and behavioralinformation from at least one of the individual and the population ofindividuals. In Block S153, the supplementary dataset preferablyincludes survey-derived data, but can additionally or alternativelyinclude any one or more of: contextual data derived from sensors,medical data, and any other suitable type of data.

In variations of Block S153 including reception of survey-derived data,the survey-derived data preferably provides physiological, demographic,and behavioral information in association with an individual.Physiological information can include information related tophysiological features (e.g., height, weight, body mass index, body fatpercent, body hair level, etc.). Demographic information can includeinformation related to demographic features (e.g., gender, age,ethnicity, marital status, number of siblings, socioeconomic status,sexual orientation, etc.). Behavioral information can includeinformation related to one or more of: health conditions (e.g., healthand disease states), living situations (e.g., living alone, living withpets, living with a significant other, living with children, etc.),dietary habits (e.g., omnivorous, vegetarian, vegan, sugar consumption,acid consumption, etc.), behavioral tendencies (e.g., levels of physicalactivity, drug use, alcohol use, etc.), different levels of mobility(e.g., related to distance traveled within a given time period),different levels of sexual activity (e.g., related to numbers ofpartners and sexual orientation), and any other suitable behavioralinformation. In one example, a survey configured to facilitategeneration of the supplementary dataset includes a question related toheight of the individual, weight of the individual, diet of theindividual, alcohol consumption of the individual, smoking behavior ofthe individual, caffeinated beverage consumption of the individual, anddiet beverage consumption of the individual. Survey-derived data canthus include quantitative data and/or qualitative data that can beconverted to quantitative data (e.g., using scales of severity, mappingof qualitative responses to quantified scores, etc.). A specific exampleof a survey is shown in FIG. 13.

In facilitating reception of survey-derived data, Block S153 can includeproviding one or more surveys to an individual, or to an entity (e.g.,healthcare provider, caretaker, spouse, relative, etc.) associated withthe individual. Surveys can be provided in person (e.g., in coordinationwith sample provision and reception from an individual), electronically(e.g., during account setup by an individual in Block S100, at anapplication executing at an electronic device of an individual), and/orin any other suitable manner.

Additionally or alternatively, portions of the supplementary dataset ofBlock S153 can be derived from sensors associated with the individual(s)(e.g., sensors of wearable computing devices, sensors of mobile devices,biometric sensors associated with the user, etc.). As such, Block S153can include receiving one or more of: physical activity- or physicalaction-related data (e.g., accelerometer and gyroscope data from amobile device or wearable electronic device of an individual),environmental data (e.g., temperature data, elevation data, climatedata, light parameter data, etc.), patient nutrition or diet-relateddata (e.g., data from food establishment check-ins, data fromspectrophotometric analysis, etc.), biometric data (e.g., data recordedthrough sensors within the patient's mobile computing device, datarecorded through a wearable or other peripheral device in communicationwith the patient's mobile computing device), location data (e.g., usingGPS elements), and any other suitable data. Additionally oralternatively, portions of the supplementary dataset can be derived frommedical record data and/or clinical data of the individual(s). As such,portions of the supplementary dataset of Block S153 can be derived fromone or more electronic health records (EHRs) of the individual(s). Thesupplementary dataset received in Block S153 can, however, comprise anyother suitable type of supplementary data.

As such, generating the analysis in Block S152 can include generatingvalues of parameters derived from features of Block S151, generation ofassociations between features (or values of parameters derived fromfeatures) and information derived from the supplementary dataset,generation of confidence metrics or measures of correlational strengthbetween microbiome-based features (or values of parameters derived fromfeatures) and behavioral or demographic characteristics derived from thesupplementary dataset, and/or any other suitable insights. In somevariations, portions of the analysis can support or provide diagnostictools that can characterize an individual (e.g., in terms of behavioraltraits, in terms of medical conditions, in terms of demographic traits,etc.) based upon their microbiome composition, and/or predict anindividual's microbiome composition based upon one or more of theirbehavioral traits, medical conditions, demographic traits, and any othersuitable traits.

In Block S152, portions of an analysis can be derived from machinelearning-based techniques, whereby input data derived from generatedfeatures can be processed with a training dataset having features linkedto candidate classifications (e.g., derived from a supplementarydataset) to provide a classification model that links microbiome-basedfeatures to other characteristics of an individual. In one variation, aclassification model generated in Block S152 can be trained to identifymicrobiome-based features and/or feature combinations that have highdegrees (or low degrees) of predictive power in accurately predicting aclassification of an individual. As such, refinement of theclassification model with the training dataset identifies feature sets(e.g., of individual features, of combinations of features) having highcorrelation with specific classifications of individuals.

Feature selection approaches can include correlation feature selection(CFS) methods, consistency methods, relief methods, information gainmethods, symmetrical uncertainty methods, and/or any other suitablemethods of feature selection. In one variation, the feature vectors caninclude features related to one or more of: microbiome diversity metrics(e.g., in relation to distribution across taxonomic groups, in relationto distribution across bacterial, viral, and/or fungal groups), presenceof taxonomic groups in one's microbiome, representation of specificgenetic sequences (e.g., 16S sequences, 18S sequences, ITS sequences,etc.) in one's microbiome, relative abundance of taxonomic groups inone's microbiome, microbiome resilience metrics (e.g., in response to aperturbation determined from the supplementary dataset), and any othersuitable features derived from the microbiome diversity dataset and/orthe supplementary dataset. Additionally, combinations of features can beused in a feature vector, wherein features can be grouped and/orweighted in providing a combined feature as part of a feature set. Forexample, one feature or feature set can include a weighted composite ofthe number of represented classes of bacteria in one's microbiome,presence of a specific genus of bacteria in one's microbiome,representation of a specific 16S sequence in one's microbiome,representation of a specific 18S sequence in one's microbiome,representation of an ITS sequence in one's microbiome, and relativeabundance of a first phylum over a second phylum of bacteria. However,the feature vectors can additionally or alternatively be determined inany other suitable manner.

As shown in FIG. 14, in one variation of Block S152 involving generationof a classification model using a machine-learning classifier, theclassification model can be generated and trained according to a randomforest predictor (RFP) algorithm that combines bagging (i.e., bootstrapaggregation) and selection of random sets of features from a trainingdataset to construct a set of decision trees, T, associated with therandom sets of features. In using a random forest algorithm, N casesfrom the set of decision trees are sampled at random with replacement tocreate a subset of decision trees, and for each node, m predictionfeatures are selected from all of the prediction features forassessment. The prediction feature that provides the best split at thenode (e.g., according to an objective function) is used to perform thesplit (e.g., as a bifurcation at the node, as a trifurcation at thenode). By sampling many times from a large dataset, the strength of theclassification model, in identifying features that are strong inpredicting classifications can be increased substantially. In thisvariation, measures to prevent bias (e.g., sampling bias) and/or accountfor an amount of bias can be included during processing to increaserobustness of the model.

While a random forest method of machine learning is described in thevariation above, Block S140 can additionally or alternatively utilizeany other suitable machine learning algorithms in forming and/ortraining the classification model. In variations, the machine learningalgorithm(s) can be characterized by a learning style including any oneor more of: supervised learning (e.g., using logistic regression, usingback propagation neural networks), unsupervised learning (e.g., using anApriori algorithm, using K-means clustering), semi-supervised learning,reinforcement learning (e.g., using a Q-learning algorithm, usingtemporal difference learning), and any other suitable learning style.Furthermore, the machine learning algorithm can implement any one ormore of: a regression algorithm (e.g., ordinary least squares, logisticregression, stepwise regression, multivariate adaptive regressionsplines, locally estimated scatterplot smoothing, etc.), aninstance-based method (e.g., k-nearest neighbor, learning vectorquantization, self-organizing map, etc.), a regularization method (e.g.,ridge regression, least absolute shrinkage and selection operator,elastic net, etc.), a decision tree learning method (e.g.,classification and regression tree, iterative dichotomiser 3, C4.5,chi-squared automatic interaction detection, decision stump, randomforest, multivariate adaptive regression splines, gradient boostingmachines, etc.), a Bayesian method (e.g., naïve Bayes, averagedone-dependence estimators, Bayesian belief network, etc.), a kernelmethod (e.g., a support vector machine, a radial basis function, alinear discriminate analysis, etc.), a clustering method (e.g., k-meansclustering, expectation maximization, etc.), an associated rule learningalgorithm (e.g., an Apriori algorithm, an Eclat algorithm, etc.), anartificial neural network model (e.g., a Perceptron method, aback-propagation method, a Hopfield network method, a self-organizingmap method, a learning vector quantization method, etc.), a deeplearning algorithm (e.g., a restricted Boltzmann machine, a deep beliefnetwork method, a convolution network method, a stacked auto-encodermethod, etc.), a dimensionality reduction method (e.g., principalcomponent analysis, partial least squares regression, Sammon mapping,multidimensional scaling, projection pursuit, etc.), an ensemble method(e.g., boosting, boostrapped aggregation, AdaBoost, stackedgeneralization, gradient boosting machine method, random forest method,etc.), and any suitable form of machine learning algorithm, some formsof which are described in U.S. App. No. 61/953,683, entitled “MultiplexMarkers” and filed on 14 Mar. 2014.

Additionally or alternatively, portions of the analysis generated inBlock S150 can be generated using statistical methods and tools,including one or more of: basic statistics, scatterplot analysis,principal component analysis (PCA), edge PCT, UniFrac analyses (e.g., tocalculate distances between identified microorganism communities usingphylogentic information), multivariate analyses, analyses of variance,cluster analysis, Kantorovich-Rubinstein metrics, and any other suitablestatistical method.

Block S160 recites: from the processing system, transmitting informationderived from values of the set of parameters to the individual, whichfunctions to share insights derived from the analysis of Block S150 withone or more individuals. In Block S160, transmitting information to anindividual can be facilitated by way of the user account for theindividual, set up in variations of Block S113, such that theinformation is accessible at an electronic device (e.g., personalcomputer, smart phone, head-mounted wearable computing device,wrist-mounted wearable computing device, tablet, laptop, netbook, etc.)of the individual. Additionally or alternatively, information can beprovided to the individual in the form of a printed report, anelectronic document (e.g., a PDF), as raw data, and/or in any othersuitable form.

In variations, the information can indicate one or more of: the presenceof one or more microorganisms in an individual's microbiome (e.g., thepresence of Streptococcus bacteria in an oral sample); the absence ofone or more microorganisms in an individual's microbiome; the abundance(e.g., relative abundance, absolute abundance) of one or moremicroorganisms in an individual's microbiome; and comparisons betweenthe microbiome composition of an individual relative to one or moresubpopulations of individuals or populations of individuals based uponany physiological, demographic, or behavioral classification.Information can additionally or alternatively be provided in Block S160in the context of average, typical, or healthy ranges. In one example,as shown in FIG. 15A, information provided to an individual can depictan amount of a given type of microorganism present in a sample from anindividual with reference to an average range of amounts of the giventype of microorganism and reference to a full range of amounts of thegiven type of microorganism from a population of individuals.

Information provided in Block S160 can additionally or alternatively beorganized into different user levels, wherein each user level can haveaccess to different data, analyses, and/or other tools. For instance,user levels can be organized according to one or more of profession(e.g., scientist, researcher, clinician, healthcare provider, etc.),status (e.g., consumer, patient), and any other classification of userlevel. For instance, in one example, scientists/researchers can bepermitted to upload research or study data, compare research or studydata to other research or study data, compare research or study data todata from different subpopulations of individuals, and predict resultsof a larger study from results of a pilot study. In another example,clinicians can be permitted to view information pertaining to patients,and patients can be permitted to share information with theirclinicians.

Information provided in Block S160 can additionally or alternatively bepresented within a certain time from receipt of a sample from anindividual (e.g. within a period of 90 days, etc.), and in variationswherein multiple samples are provided by an individual, information canbe provided with a time-varying and/or sample-site adjustable component.Furthermore, information can be provided with respect to any suitablenumber of microorganism taxonomic groups (e.g., from 1 to 10,000species, from 10,000 genera, etc.).

In Block S160, information can be provided (e.g., in a printed report,in an electronic document) or rendered at an electronic display usingvisualization tools including one or more of: visualization tools fortaxonomic data (e.g., tables and/or graphics showing domain, kingdom,phylum, class, order, family, genus, species, and/or subspeciesrelationships, an example of which is shown in FIG. 15F), phylogenetictrees, cladograms, dendrograms, pie charts, bar charts, scatter plots,and any other suitable visualization tool. Furthermore, a user interfaceassociated with a user account can provide controls, examples of whichare shown in FIG. 15B, to adjust levels of detail provided to theindividual, to adjust types of comparison information provided to theindividual, to adjust a taxonomy level of an analysis provided to theindividual, and/or to adjust any other suitable parameter pertaining toinformation provided to the individual.

In examples shown in FIG. 15C, information provided in Block S160 can berendered at a display in the form of one or more of: a scatterplot 610,a network chart 620, a pie chart 630, a graphic showing microbiome-basedparameters relative to collection sites of an individual 640, a set ofcomparison diagrams between microbiome compositional features of anindividual in comparison to one or more subpopulations of individuals650, and a set of comparison matrices between microbiome compositionalfeatures of an individual in comparison to one or more subpopulations ofindividuals 660. In one example, as shown in FIG. 15D, Block S160 caninclude rendering a pie chart 710 displaying microbiome compositionalinformation for a sample from an individual, with a legend 720describing represented microbiome components. In another example, asshown in FIG. 15B, Block S160 can include rendering a set of pie charts810, 820 comparing the microbiome composition of a sample from anindividual to an average of all samples provided from a population ofindividuals at a taxonomic level (e.g., genus level), in coordinationwith a user interface 830 that allows an individual to receiveinformation at other taxonomic levels (e.g., the domain level, thephylum level, the class level, the order level, the family level, thegenus level, the species level, the sub-species level) upon receiving ofan input at the user interface by the individual. In yet anotherexample, as shown in FIG. 15E, Block S160 can include rendering a set ofbar charts 910, 920, 930, 940 comparing the microbiome composition of asample from an individual to the average microbiome composition for asubpopulation of healthy omnivores, the average microbiome compositionfor a subpopulation of vegetarians, and the average microbiomecomposition for the entire population of individuals analyzed.

2. Specific Application

A specific application of example workflows is described, wherein in aworkflow, an individual receives a sampling kit, interacts with thesampling kit, and provides samples for analysis by using components ofthe sampling kit. In the workflow, the sample(s) from an individual isreceived, processed, analyzed, and used to provide information to theindividual.

In the specific application of the first workflow, an individualreceives a sampling kit, transmits one or more samples from one or morecollection sites into sample containers of the sampling kit, and returnsthe sample containers to a sample handling network by way of packagingreceptacles included in the sampling kit. Registration codes (e.g.,barcodes) associated with the sampling kit and the sample container(s)are logged, at the sample handling network, for tracking. Samples fromthe individual are then introduced into an automated sample handlingworkflow implementing a sample processing module and a processingsystem, wherein nucleic acids from the samples are purified, amplified,tagged, and sequenced. Data derived from sequenced nucleic acids is thenassociated with samples based upon identifiers (e.g., identificationsequences, barcodes, tags, etc.) and analyzed to derive microbiomeinformation. Information pertaining to the microbiome of the individualis then presented to the individual by way of an interactive websitethat provides renderings of graphs, charts, and comparisons between themicrobiome of each sample from the individual, and relevantsubpopulations of individuals, relevant ranges of metrics, and/orrelevant microbiome-based studies.

The method 100 and/or system 200 of the embodiments can be embodiedand/or implemented at least in part as a machine configured to receive acomputer-readable medium storing computer-readable instructions. Theinstructions can be executed by computer-executable componentsintegrated with the application, applet, host, server, network, website,communication service, communication interface,hardware/firmware/software elements of a patient computer or mobiledevice, or any suitable combination thereof. Other systems and methodsof the embodiments can be embodied and/or implemented at least in partas a machine configured to receive a computer-readable medium storingcomputer-readable instructions. The instructions can be executed bycomputer-executable components integrated by computer-executablecomponents integrated with apparatuses and networks of the typedescribed above. The computer-readable medium can be stored on anysuitable computer readable media such as RAMs, ROMs, flash memory,EEPROMs, optical devices (CD or DVD), hard drives, floppy drives, or anysuitable device. The computer-executable component can be a processor,though any suitable dedicated hardware device can (alternatively oradditionally) execute the instructions.

The FIGURES illustrate the architecture, functionality and operation ofpossible implementations of systems, methods and computer programproducts according to preferred embodiments, example configurations, andvariations thereof. In this regard, each block in the flowchart or blockdiagrams may represent a module, segment, step, or portion of code,which comprises one or more executable instructions for implementing thespecified logical function(s). It should also be noted that, in somealternative implementations, the functions noted in the block can occurout of the order noted in the FIGURES. For example, two blocks shown insuccession may, in fact, be executed substantially concurrently, or theblocks may sometimes be executed in the reverse order, depending uponthe functionality involved. It will also be noted that each block of theblock diagrams and/or flowchart illustration, and combinations of blocksin the block diagrams and/or flowchart illustration, can be implementedby special purpose hardware-based systems that perform the specifiedfunctions or acts, or combinations of special purpose hardware andcomputer instructions.

As a person skilled in the art will recognize from the previous detaileddescription and from the figures and claims, modifications and changescan be made to the embodiments of the invention without departing fromthe scope of this invention as defined in the following claims.

We claim:
 1. A method for processing a nucleic acid sample, comprisinggenetic content of a microorganism ecosystem, from an individual, themethod comprising: providing a sampling kit to the individual at aremote location, the sampling kit including a sample container having apre-process reagent component and configured to receive a sample from acollection site of the individual; from the remote location, receivingthe sample container with the sample from the collection site of theindividual; generating a solution upon combination of the sample with afirst substrate set having a first primer type, associated with a firstnucleic acid marker of a first microorganism portion of the sample andisolated to the first substrate set, and a second substrate set having asecond primer type associated with a second nucleic acid marker of asecond microorganism portion of the sample and isolated to the secondsubstrate set; simultaneously amplifying genetic content associated withthe first nucleic acid marker by way of the first substrate set andgenetic content associated with the second nucleic acid marker by way ofthe second substrate set in a process chamber, for facilitatingsequencing with a next generation sequencing platform; generating amicrobiome sequence dataset based upon sequencing, with the nextgeneration sequencing platform, genetic content associated with thefirst and the second nucleic acid markers; and at one or more computingdevices, generating an analysis characterizing the first microorganismportion and the second microorganism portion based upon the microbiomesequence dataset derived from the individual.
 2. The method of claim 1,wherein the first substrate set and the second substrate set arefree-floating in the solution, upon combination of the sample with thefirst substrate set and the second substrate set.
 3. The method of claim2, wherein the first primer type comprises a first primer pair includinga first forward primer and a first reverse primer, and wherein thesecond primer type comprises a second primer pair including a secondforward primer and a second reverse primer.
 4. The method of claim 3,wherein each of the first substrate set has a first physical propertyand each of the second substrate set has a second physical property, andwherein the first physical property and the second physical propertyfacilitate simultaneous amplification of genetic content associated withthe first nucleic acid marker and genetic content associated with thesecond nucleic acid marker within a single process chamber.
 5. Themethod of claim 4, wherein the first physical property comprises a firstmorphology and the second physical property comprises a secondmorphology different from the first morphology, and wherein each of thefirst morphology and the second morphology prevent primer-primerinteractions between the first primer type and the second primer type.6. The method of claim 4, wherein the first physical property comprisesa first magnetic property that enables the first substrate set to beseparated from the second substrate set during simultaneousamplification of genetic content associated with the first nucleic acidmarker and genetic content associated with the second nucleic acidmarker.
 7. The method of claim 6, further comprising providing amagnetic field proximal the process chamber, thereby physicallyseparating the first substrate set from the second substrate duringsimultaneous amplification of genetic content associated with the firstnucleic acid marker and genetic content associated with the secondnucleic acid marker within the process chamber.
 8. The method of claim1, wherein at least one of the first substrate set and the secondsubstrate set comprises a two-dimensional substrate.
 9. The method ofclaim 8, wherein the first substrate set and the second substrate arespatially separated from each other but are indirectly coupled to eachother by occupying different regions of a larger substrate.
 10. Themethod of claim 1, wherein receiving the sample container with thesample from the collection site of the individual comprises receivingthe sample, prepared to a pre-processed state of lysis by theindividual.
 11. A system for processing a nucleic acid sample,comprising genetic content of a microorganism ecosystem, from anindividual, the system comprising: a sampling kit including a samplecontainer having a lysing component and a sample preservation componentand configured to receive a sample from a collection site of theindividual; and a sample processing system comprising at least one of aprocess chamber and a bridge amplification substrate for facilitatingsequencing with a next generation sequencing platform, wherein thesample processing system facilitates: with a laboratory automationworkstation of the sample processing system, generating a solution uponcombination of the sample with a first substrate set having a firstprimer type, associated with a first nucleic acid marker of a firstmicroorganism portion of the sample and isolated to the first substrateset, and a second substrate set having a second primer type associatedwith a second nucleic acid marker of a second microorganism portion ofthe sample and isolated to the second substrate set, simultaneouslyamplifying genetic content associated with the first nucleic acid markerby way of the first substrate set and genetic content associated withthe second nucleic acid marker by way of the second substrate set in atleast one of the process chamber and the bridge amplification substrate,and with one or more computing devices of the sample processing system,generating a microbiome sequence dataset based upon sequencing, with thenext generation sequencing platform, genetic content associated with thefirst and the second nucleic acid markers.
 12. The system of claim 11,wherein the first substrate set and the second substrate set arefree-floating in the solution, upon combination of the sample with thefirst substrate set and the second substrate set.
 13. The system ofclaim 12, wherein each of the first substrate set has a first physicalproperty and each of the second substrate set has a second physicalproperty, and wherein the first physical property and the secondphysical property facilitate simultaneous amplification of geneticcontent associated with the first nucleic acid marker and geneticcontent associated with the second nucleic acid marker within a singleinstance of the at least one of the process chamber and the bridgeamplification substrate.
 14. The system of claim 13, wherein the firstphysical property comprises a first morphology and the second physicalproperty comprises a second morphology different from the firstmorphology, and wherein each of the first morphology and the secondmorphology prevent primer-primer interactions between the first primertype and the second primer type.
 15. The system of claim 14, wherein thefirst physical property comprises a first magnetic property that enablesthe first substrate set to be separated from the second substrate setduring simultaneous amplification of genetic content associated with thefirst nucleic acid marker and genetic content associated with the secondnucleic acid marker.
 16. The system of claim 15, wherein the sampleprocessing system includes magnet that provides a magnetic fieldproximal the process chamber, thereby physically separating the firstsubstrate set from the second substrate during simultaneousamplification of genetic content associated with the first nucleic acidmarker and genetic content associated with the second nucleic acidmarker within the at least one of the process chamber and the bridgeamplification substrate.
 17. The system of claim 11, wherein at leastone of the first substrate set and the second substrate set comprises atwo-dimensional substrate.
 18. The system of claim 11 wherein the firstsubstrate set and the second substrate are spatially separated from eachother, but are indirectly coupled to each other by occupying differentregions of a larger substrate.
 19. The system of claim 11, wherein theone or more computing devices of the sample processing system furthercomprise an analysis generating operation mode that generates ananalysis characterizing the first microorganism portion and the secondmicroorganism portion based upon the microbiome sequence dataset derivedfrom the individual.
 20. The system of claim 19, wherein the one or morecomputing devices of sample processing system further comprise anoperation mode that receives a supplementary dataset comprising surveydata with information regarding demographic and behavioral informationof each of a population individuals, and trains a machine-learningclassifier to generate a ranking of features, associated with at leastone of the first microorganism portion and the second microorganismportion and derived from the microbiome sequence dataset, wherein theranking of features organizes features according to predictive power inpredicting at least one of demographic classifications and behavioralclassifications determined based upon the supplementary dataset.